├── .github └── workflows │ ├── deploy.yml │ └── test.yml ├── .gitignore ├── .gitpod.yml ├── LICENSE.txt ├── README.md ├── channel-duplication.nf ├── collect-into-file.nf ├── conditional-process.nf ├── conditional-process2.nf ├── conditional-process3.nf ├── conditional-resources.nf ├── create-key-to-combine-channels.nf ├── data ├── alignment │ ├── kidney.bai │ ├── kidney.bam │ ├── lung.bai │ └── lung.bam ├── hello.txt ├── index.csv ├── poem.txt ├── prots │ ├── prot_1.fa │ ├── prot_2.fa │ ├── prot_3.fa │ └── sample.fa └── reads │ ├── 110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_1.fq.gz │ ├── 110101_I315_FC816RLABXX_L1_HUMrutRGXDIAAPE_2.fq.gz │ ├── 110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_1.fq.gz │ ├── 110105_I186_FC812MWABXX_L8_HUMrutRGVDIABPE_2.fq.gz │ ├── 110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_1.fq.gz │ ├── 110121_I288_FC81DE8ABXX_L3_HUMrutRGXDIAAPE_2.fq.gz │ ├── 110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_1.fq.gz │ ├── 110122_I329_FC81DB5ABXX_L6_HUMrutRGVDIAAPE_2.fq.gz │ ├── 110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_1.fq.gz │ ├── 110128_I481_FC819P0ABXX_L5_HUMrutRGWDIAAPE_2.fq.gz │ └── sample.fq.gz ├── docs ├── channel-duplication.md ├── collect-into-file.md ├── conditional-process-dynamic.md ├── conditional-process.md ├── conditional-resources.md ├── create-key-to-combine-channels.md ├── feedback-loop.md ├── ignore-failing-process.md ├── index.md ├── optional-input.md ├── optional-output.md ├── process-collect.md ├── process-get-workdir.md ├── process-into-groups.md ├── process-per-csv-record.md ├── process-per-file-chunk.md ├── process-per-file-output.md ├── process-per-file-pairs.md ├── process-per-file-path.md ├── process-per-file-range.md ├── process-when-empty.md ├── publish-matching-glob.md ├── publish-process-outputs.md ├── publish-rename-outputs.md ├── skip-process-execution.md ├── sort-filepairs-by-samplename.md ├── state-dependency.md ├── task-batching.md └── workflow-grouping.md ├── feedback-loop-process.nf ├── feedback-loop-workflow.nf ├── ignore-failing-process.nf ├── mkdocs.yml ├── nextflow.config ├── optional-input.nf ├── optional-output.nf ├── process-collect.nf ├── process-get-workdir.nf ├── process-into-groups.nf ├── process-per-csv-record.nf ├── process-per-file-chunk.nf ├── process-per-file-output.nf ├── process-per-file-pairs-custom.nf ├── process-per-file-pairs.nf ├── process-per-file-path.nf ├── process-per-file-range.nf ├── process-when-empty.nf ├── publish-matching-glob.nf ├── publish-process-outputs.nf ├── publish-rename-outputs-subdirs.nf ├── publish-rename-outputs.nf ├── scripts ├── cleanup.sh └── test.sh ├── skip-process-execution.nf ├── sort-filepairs-by-samplename.nf ├── state-dependency.nf ├── task-batching.nf └── workflow-grouping.nf /.github/workflows/deploy.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nextflow-io/patterns/HEAD/.github/workflows/deploy.yml 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