gitpod /workspace/nf-core-smrnaseq (dev) $ nf-core --verbose lint ,--./,-. ___ __ __ __ ___ /,-._.--~\ |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' nf-core/tools version 2.13.1 - https://nf-co.re DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/workspace/nf-core-smrnaseq, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: .nf-core.yml utils.py:1043 DEBUG Got '.' as path utils.py:230 DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-575d1e3c2efc6b89a4afefc6e.json utils.py:264 DEBUG Popen(['git', 'version'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'fetch', '-v', '--progress', '--', 'origin'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=True) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Using config file: .nf-core.yml utils.py:1043 DEBUG The following files were modified by prettier: lint_utils.py:87 modules.json DEBUG Got '.' as path utils.py:230 DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-575d1e3c2efc6b89a4afefc6e.json utils.py:264 DEBUG Registry set to quay.io __init__.py:139 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Using config file: .nf-core.yml utils.py:1043 DEBUG The following files were modified by prettier: modules.json DEBUG Got '.' as path utils.py:230 DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-575d1e3c2efc6b89a4afefc6e.json utils.py:264 DEBUG Registry set to quay.io __init__.py:139 DEBUG Using config file: .nf-core.yml utils.py:1043 DEBUG Using config file: .nf-core.yml utils.py:1043 INFO Testing pipeline: . __init__.py:300 DEBUG Running lint test: files_exist __init__.py:363 DEBUG Found plugins in nextflow.config with value nf-validation files_exist.py:253 DEBUG Running lint test: nextflow_config __init__.py:363 DEBUG JSON file loaded: nextflow_schema.json schema.py:117 DEBUG Running lint test: files_unchanged __init__.py:363 DEBUG No tools config file found: .nf-core.yml utils.py:1034 DEBUG Logo already exists in cache at: /home/gitpod/.cache/nfcore/logo/nf-core-smrnaseq_logo_light_2300.png. Reusing this file. create_logo.py:65 DEBUG STREAM b'IHDR' 16 13 PngImagePlugin.py:191 DEBUG STREAM b'iCCP' 41 379 PngImagePlugin.py:191 DEBUG iCCP profile name b'ICC Profile' PngImagePlugin.py:394 DEBUG Compression method 0 PngImagePlugin.py:395 DEBUG STREAM b'IDAT' 432 65536 PngImagePlugin.py:191 DEBUG Saved logo to: '/tmp/tmpmw3ju5mz/nf-core-smrnaseq/assets/nf-core-smrnaseq_logo_light.png' create_logo.py:107 DEBUG Logo already exists in cache at: /home/gitpod/.cache/nfcore/logo/nf-core-smrnaseq_logo_dark_600.png. Reusing this file. create_logo.py:65 DEBUG STREAM b'IHDR' 16 13 PngImagePlugin.py:191 DEBUG STREAM b'iCCP' 41 379 PngImagePlugin.py:191 DEBUG iCCP profile name b'ICC Profile' PngImagePlugin.py:394 DEBUG Compression method 0 PngImagePlugin.py:395 DEBUG STREAM b'IDAT' 432 28913 PngImagePlugin.py:191 DEBUG Saved logo to: '/tmp/tmpmw3ju5mz/nf-core-smrnaseq/docs/images/nf-core-smrnaseq_logo_dark.png' create_logo.py:107 DEBUG Logo already exists in cache at: /home/gitpod/.cache/nfcore/logo/nf-core-smrnaseq_logo_light_600.png. Reusing this file. create_logo.py:65 DEBUG STREAM b'IHDR' 16 13 PngImagePlugin.py:191 DEBUG STREAM b'iCCP' 41 379 PngImagePlugin.py:191 DEBUG iCCP profile name b'ICC Profile' PngImagePlugin.py:394 DEBUG Compression method 0 PngImagePlugin.py:395 DEBUG STREAM b'IDAT' 432 24630 PngImagePlugin.py:191 DEBUG Saved logo to: '/tmp/tmpmw3ju5mz/nf-core-smrnaseq/docs/images/nf-core-smrnaseq_logo_light.png' create_logo.py:107 DEBUG Using config file: /tmp/tmpmw3ju5mz/nf-core-smrnaseq/.nf-core.yml utils.py:1043 DEBUG Files are almost the same. Will pass: assets/nf-core-smrnaseq_logo_light.png files_unchanged.py:170 DEBUG Files are almost the same. Will pass: docs/images/nf-core-smrnaseq_logo_dark.png files_unchanged.py:170 DEBUG Running lint test: actions_ci __init__.py:363 DEBUG Running lint test: actions_awstest __init__.py:363 DEBUG Running lint test: actions_awsfulltest __init__.py:363 DEBUG Running lint test: readme __init__.py:363 DEBUG Running lint test: pipeline_todos __init__.py:363 DEBUG Running lint test: pipeline_name_conventions __init__.py:363 DEBUG Running lint test: template_strings __init__.py:363 DEBUG Running lint test: schema_lint __init__.py:363 DEBUG Got '.' as path utils.py:230 DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-575d1e3c2efc6b89a4afefc6e.json utils.py:264 DEBUG Running lint test: schema_params __init__.py:363 DEBUG Got '.' as path utils.py:230 DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-575d1e3c2efc6b89a4afefc6e.json utils.py:264 DEBUG Running lint test: system_exit __init__.py:363 DEBUG Running lint test: schema_description __init__.py:363 DEBUG Got '.' as path utils.py:230 DEBUG Found a config cache, loading: /home/gitpod/.nextflow/nf-core/wf-config-cache-575d1e3c2efc6b89a4afefc6e.json utils.py:264 DEBUG Running lint test: actions_schema_validation __init__.py:363 DEBUG Starting new HTTPS connection (1): json.schemastore.org:443 connectionpool.py:1052 DEBUG https://json.schemastore.org:443 "GET /github-workflow HTTP/1.1" 200 10587 connectionpool.py:546 DEBUG Running lint test: merge_markers __init__.py:363 DEBUG Running lint test: modules_json __init__.py:363 DEBUG Running lint test: multiqc_config __init__.py:363 DEBUG Running lint test: modules_structure __init__.py:363 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/blat:36--0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/blat:36--0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/blat:36--0 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/blat:36--0/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/blat?tab=tags&tag=36--0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/blat:36--0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/blat HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/bowtie2:2.4.5--py39hd2f7db1_2 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie2:2.4.5--py39hd2f7db1_2 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie2:2.4.5--py39hd2f7db1_2/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/bowtie2?tab=tags&tag=2.4.5--py39hd2f7db1_2 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/bowtie2:2.4.5--py39hd2f7db1_2, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/bowtie:1.3.1--py310h7b97f60_6 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/bowtie:1.3.1--py310h7b97f60_6, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie:1.3.1--py310h7b97f60_6 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie:1.3.1--py310h7b97f60_6/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/bowtie?tab=tags&tag=1.3.1--py310h7b97f60_6 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/bowtie:1.3.1--py310h7b97f60_6, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/bowtie HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/bowtie2:2.4.5--py39hd2f7db1_2 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie2:2.4.5--py39hd2f7db1_2 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie2:2.4.5--py39hd2f7db1_2/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/bowtie2?tab=tags&tag=2.4.5--py39hd2f7db1_2 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/bowtie2:2.4.5--py39hd2f7db1_2, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3?tab=tags&tag=40128b496751b037e2bd85f6789e83d4ff8a4837-0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:40128b496751b037e2bd85f6789e83d4ff8a4837-0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/samtools HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/bowtie:1.3.1--py310h7b97f60_6 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/bowtie:1.3.1--py310h7b97f60_6, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie:1.3.1--py310h7b97f60_6 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie:1.3.1--py310h7b97f60_6/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/bowtie?tab=tags&tag=1.3.1--py310h7b97f60_6 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/bowtie:1.3.1--py310h7b97f60_6, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/bowtie HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/r-data.table:1.12.2 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/r-data.table:1.12.2, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/r-data.table:1.12.2 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/r-data.table:1.12.2/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/r-data.table?tab=tags&tag=1.12.2 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/r-data.table:1.12.2, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1?tab=tags&tag=f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/mulled-v2-419bd7f10b2b902489ac63bbaafc7db76f8e0ae1:f5ff7de321749bc7ae12f7e79a4b581497f4c8ce-0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/bioconductor-limma HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/bioconductor-edger HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/bowtie2:2.4.5--py39hd2f7db1_2 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/bowtie2:2.4.5--py39hd2f7db1_2, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie2:2.4.5--py39hd2f7db1_2 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/bowtie2:2.4.5--py39hd2f7db1_2/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/bowtie2?tab=tags&tag=2.4.5--py39hd2f7db1_2 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/bowtie2:2.4.5--py39hd2f7db1_2, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/fastx_toolkit:0.0.14--hdbdd923_11 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/fastx_toolkit:0.0.14--hdbdd923_11, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/fastx_toolkit:0.0.14--hdbdd923_11 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/fastx_toolkit:0.0.14--hdbdd923_11/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/fastx_toolkit?tab=tags&tag=0.0.14--hdbdd923_11 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/fastx_toolkit:0.0.14--hdbdd923_11, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/fastx_toolkit HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/mirdeep2:2.0.1.3--hdfd78af_1 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.3--hdfd78af_1, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/mirdeep2:2.0.1.3--hdfd78af_1 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/mirdeep2:2.0.1.3--hdfd78af_1/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/mirdeep2?tab=tags&tag=2.0.1.3--hdfd78af_1 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/mirdeep2:2.0.1.3--hdfd78af_1, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/mirdeep2 HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/bioconvert:1.1.1--pyhdfd78af_0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/bioconvert:1.1.1--pyhdfd78af_0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/bioconvert:1.1.1--pyhdfd78af_0 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/bioconvert:1.1.1--pyhdfd78af_0/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/bioconvert?tab=tags&tag=1.1.1--pyhdfd78af_0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/bioconvert:1.1.1--pyhdfd78af_0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/bioconvert HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/mirdeep2:2.0.1.3--hdfd78af_1 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.3--hdfd78af_1, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/mirdeep2:2.0.1.3--hdfd78af_1 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/mirdeep2:2.0.1.3--hdfd78af_1/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/mirdeep2?tab=tags&tag=2.0.1.3--hdfd78af_1 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/mirdeep2:2.0.1.3--hdfd78af_1, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/mirdeep2 HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385?tab=tags&tag=63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/samtools HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/seqkit:2.6.1--h9ee0642_0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/seqkit:2.6.1--h9ee0642_0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/seqkit:2.6.1--h9ee0642_0 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/seqkit:2.6.1--h9ee0642_0/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/seqkit?tab=tags&tag=2.6.1--h9ee0642_0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/seqkit:2.6.1--h9ee0642_0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/seqkit HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/seqcluster:1.2.9--pyh5e36f6f_0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/seqcluster:1.2.9--pyh5e36f6f_0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/seqcluster:1.2.9--pyh5e36f6f_0 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/seqcluster:1.2.9--pyh5e36f6f_0/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/seqcluster?tab=tags&tag=1.2.9--pyh5e36f6f_0 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/seqcluster:1.2.9--pyh5e36f6f_0, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/seqcluster HTTP/1.1" 200 None connectionpool.py:546 DEBUG Starting new HTTPS connection (1): depot.galaxyproject.org:443 connectionpool.py:1052 DEBUG https://depot.galaxyproject.org:443 "HEAD /singularity/mirtrace:1.0.1--hdfd78af_1 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://depot.galaxyproject.org/singularity/mirtrace:1.0.1--hdfd78af_1, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): quay.io:443 connectionpool.py:1052 DEBUG https://quay.io:443 "HEAD /biocontainers/mirtrace:1.0.1--hdfd78af_1 HTTP/1.1" 308 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /biocontainers/mirtrace:1.0.1--hdfd78af_1/ HTTP/1.1" 302 0 connectionpool.py:546 DEBUG https://quay.io:443 "HEAD /repository/biocontainers/mirtrace?tab=tags&tag=1.0.1--hdfd78af_1 HTTP/1.1" 200 0 connectionpool.py:546 DEBUG Connected to URL: https://quay.io/biocontainers/mirtrace:1.0.1--hdfd78af_1, status_code: 200 main_nf.py:332 DEBUG Starting new HTTPS connection (1): api.anaconda.org:443 connectionpool.py:1052 DEBUG https://api.anaconda.org:443 "GET /package/bioconda/mirtrace HTTP/1.1" 200 None connectionpool.py:546 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/cat/cat'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/cat/cat'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', '9437e6053dccf4aafa022bfd6e7e9de67e625af8'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/cat/fastq'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/cat/fastq'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', '0997b47c93c06b49aa7b3fefda87e728312cf2ca'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/fastp'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/fastp'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', '003920c7f9a8ae19b69a97171922880220bedf56'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/fastqc'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/fastqc'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/multiqc'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/multiqc'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'b7ebe95761cd389603f9cc0e0dc384c0f663815a'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/samtools/flagstat'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/samtools/flagstat'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'f4596fe0bdc096cf53ec4497e83defdb3a94ff62'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/samtools/idxstats'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/samtools/idxstats'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'f4596fe0bdc096cf53ec4497e83defdb3a94ff62'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/samtools/index'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/samtools/index'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'f4596fe0bdc096cf53ec4497e83defdb3a94ff62'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/samtools/sort'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/samtools/sort'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'f4596fe0bdc096cf53ec4497e83defdb3a94ff62'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/samtools/stats'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/samtools/stats'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'f4596fe0bdc096cf53ec4497e83defdb3a94ff62'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/umicollapse'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/umicollapse'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'ba3f3df395d2719dcef5c67189042a1dc555c701'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/umitools/extract'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/umitools/extract'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'ff7e93715a2acecf3f143ec78c9858deba2984d0'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/nf-core/untarfiles'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'modules/untarfiles'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', '3f5420aa22e00bd030a2556dfdffc9e164ec0ec5'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'subworkflows/nf-core/bam_sort_stats_samtools'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'subworkflows/nf-core/bam_stats_samtools'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'subworkflows/nf-core/fastq_fastqc_umitools_fastp'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'subworkflows/nf-core/utils_nextflow_pipeline'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'subworkflows/nf-core/utils_nfcore_pipeline'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'merge', 'origin/master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Using config file: /home/gitpod/.config/nfcore/nf-core/modules/.nf-core.yml utils.py:1043 DEBUG Popen(['git', 'checkout', 'master'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch-check'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'rev-list', '89cf292ab826db67279cf11339c5afc53a9e419d', '--', 'subworkflows/nf-core/utils_nfvalidation_plugin'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=None, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Popen(['git', 'cat-file', '--batch'], cwd=/home/gitpod/.config/nfcore/nf-core/modules, stdin=, shell=False, universal_newlines=False) cmd.py:1057 DEBUG Printing final results __init__.py:394 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 ╭─ [?] 1 Pipeline Test Ignored ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ │ │ nextflow_config: Config default ignored: params.fastp_known_mirna_adapters │ │ │ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 ╭─ [!] 4 Pipeline Test Warnings ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ │ │ readme: README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release). │ │ pipeline_todos: TODO string in main.nf: Optionally add in-text citation tools to this list. │ │ pipeline_todos: TODO string in main.nf: Optionally add bibliographic entries to this list. │ │ pipeline_todos: TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled! │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────��──────────────────────────────────────────────────────────────────────────────────────────╯ DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 ╭─ [✗] 1 Pipeline Test Failed ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ │ │ files_unchanged: docs/images/nf-core-smrnaseq_logo_light.png does not match the template │ │ │ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ DEBUG Printing final results __init__.py:201 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 ╭─ [!] 10 Module Test Warnings ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ ╷ ╷ │ │ Module name │ File path │ Test message │ │╶─────────────────────────┼────────────────────────────────────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│ │ bowtie_map_mirna │ modules/local/bowtie_map_mirna.nf │ Conda update: bioconda::samtools 1.13 -> 1.19.2 │ │ mirdeep2_mapper │ modules/local/mirdeep2_mapper.nf │ Conda update: bioconda::mirdeep2 2.0.1.3 -> 2.0.1.2 │ │ mirdeep2_run │ modules/local/mirdeep2_run.nf │ Conda update: bioconda::mirdeep2 2.0.1.3 -> 2.0.1.2 │ │ mirtop_quant │ modules/local/mirtop_quant.nf │ Conda update: bioconda::samtools 1.15.1 -> 1.19.2 │ │ parse_fasta_mirna │ modules/local/parse_fasta_mirna.nf │ Conda update: bioconda::seqkit 2.6.1 -> 2.8.0 │ │ mirdeep2_mapper │ modules/local/mirdeep2_mapper.nf │ 'meta' map not emitted in output channel(s) │ │ fastp │ modules/nf-core/fastp │ New version available │ │ samtools/sort │ modules/nf-core/samtools/sort │ New version available │ │ umicollapse │ modules/nf-core/umicollapse │ New version available │ │ umitools/extract │ modules/nf-core/umitools/extract │ New version available │ │ ╵ ╵ │ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────��───────────────────────────────────────────────────────────────────────────╯ DEBUG Printing final results __init__.py:201 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 ╭─ [!] 12 Subworkflow Test Warnings ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ ╷ ╷ │ │ Subworkflow name │ File path │ Test message │ │╶─────────────────────────────┼──────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│ │ mirtrace │ subworkflows/local/mirtrace.nf │ Subworkflow includes less than two modules │ │ contaminant_filter │ subworkflows/local/contaminant_filter.nf │ Included component 'BLAT_CDNA' not used in main.nf │ │ contaminant_filter │ subworkflows/local/contaminant_filter.nf │ Included component 'FILTER_STATS' not used in main.nf │ │ contaminant_filter │ subworkflows/local/contaminant_filter.nf │ Included component 'INDEX_RRNA' not used in main.nf │ │ contaminant_filter │ subworkflows/local/contaminant_filter.nf │ Included component 'MAP_RRNA' not used in main.nf │ │ contaminant_filter │ subworkflows/local/contaminant_filter.nf │ Included component 'BLAT_CDNA' versions are not added in main.nf │ │ contaminant_filter │ subworkflows/local/contaminant_filter.nf │ Included component 'FILTER_STATS' versions are not added in main.nf │ │ contaminant_filter │ subworkflows/local/contaminant_filter.nf │ Included component 'INDEX_RRNA' versions are not added in main.nf │ │ contaminant_filter │ subworkflows/local/contaminant_filter.nf │ Included component 'MAP_RRNA' versions are not added in main.nf │ │ mirtrace │ subworkflows/local/mirtrace.nf │ Included component 'MIRTRACE_RUN' versions are not added in main.nf │ │ bam_sort_stats_samtools │ subworkflows/nf-core/bam_sort_stats_samtools │ New version available │ │ fastq_fastqc_umitools_fastp │ subworkflows/nf-core/fastq_fastqc_umitools_fastp │ New version available │ │ ╵ ╵ │ ╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 DEBUG entering code: StateBlock(line=0,level=0,tokens=0), 0, 1, False code.py:10 DEBUG entering fence: StateBlock(line=0,level=0,tokens=0), 0, 1, False fence.py:10 DEBUG entering blockquote: StateBlock(line=0,level=0,tokens=0), 0, 1, False blockquote.py:13 DEBUG entering hr: StateBlock(line=0,level=0,tokens=0), 0, 1, False hr.py:14 DEBUG entering list: StateBlock(line=0,level=0,tokens=0), 0, 1, False list.py:102 DEBUG entering reference: StateBlock(line=0,level=0,tokens=0), 0, 1, False reference.py:10 DEBUG entering html_block: StateBlock(line=0,level=0,tokens=0), 0, 1, False html_block.py:35 DEBUG entering heading: StateBlock(line=0,level=0,tokens=0), 0, 1, False heading.py:13 DEBUG entering lheading: StateBlock(line=0,level=0,tokens=0), 0, 1, False lheading.py:10 DEBUG entering paragraph: StateBlock(line=0,level=0,tokens=0), 0, 1, False paragraph.py:10 ╭─ [✗] 1 Subworkflow Test Failed ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │ ╷ ╷ │ │ Subworkflow name │ File path │ Test message │ │╶─────────────────────────────┼──────────────────────────────────────────────────────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╴│ │ bam_sort_stats_samtools │ subworkflows/nf-core/bam_sort_stats_samtools/main.nf │ Local copy of subworkflow does not match remote │ │ ╵ ╵ │ ╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────��────────────────────────────────────────────╯ ╭───────────────────────╮ │ LINT RESULTS SUMMARY │ ├───────────────────────┤ │ [✔] 632 Tests Passed │ │ [?] 1 Test Ignored │ │ [!] 26 Test Warnings │ │ [✗] 2 Tests Failed │ ╰───────────────────────╯ Tip: Some of these linting errors can automatically be resolved with the following command: nf-core lint --fix files_unchanged