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nf-core_modules/tests/modules/lima/test.yml

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New module: `LIMA` (#719) * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 🐛 FIX: Fill contains args * 📦 NEW: Add module lima * 👌 IMPROVE: Move .pbi output to reports channel * 🐛 FIX: Fix report channel definition * 👌IMPROVE; Remove options from command line update test script with removed options * 🐛 FIX: Add pbi input * 👌 IMPROVE: Add parallelization to lima * 👌 IMPROVE: Add some pacbio test files * 🐛 FIX: Add Pacbio index to test_data.config * 👌 IMPROVE: Re add 10000 data test * 👌 IMPROVE: Add some pbindex * 🐛 FIX: Add pbi extension to files * 👌 IMPROVE: The accept one channel (primers move into the first channel) * 👌 IMPROVE: Assign a value channel for pimers Improve code workflow readability * 👌 IMPROVE: Update module to last template version * 🐛 FIX: Correct Singularity and Docker URL * 👌 IMPROVE: Update to the last version of modules template * 👌 IMPROVE: Update test_data.config * 👌 IMPROVE: Remove pbi from input files * 👌 IMPROVE: Final version of test datasets config * 👌 IMPROVE: Remove useless index + Fix Typos * 🐛 FIX: Fill contains args * 👌 IMPROVE: Add channel for each output * 👌 IMPROVE: Remove comments * 🐛 FIX: Clean test_data.config * Update modules/lima/main.nf Add meta to each output Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update modules/lima/main.nf Remove useless parenthesis Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * 🐛 FIX: Keep version number only * 🐛 FIX: Reintegrate prefix variable and use it to define output file name * 👌 IMPROVE: add suffix arg to check output files names * 👌 IMPROVE: Use prefix for output filename * 🐛 FIX: Set optional output Allow usage of different input formats * 👌 IMPROVE: Update meta file * 👌 IMPROVE: Update test One test for each input file type * 👌 IMPROVE: add fasta, fastq.gz, fastq, fastq.gz test files * 👌 IMPROVE: Update with last templates / Follow new version.yaml rule * 🐛 FIX: Fix typos and include getProcessName function * 👌 IMPROVE: Update .gitignore * 👌 IMPROVE: Using suffix to manage output was not a my best idea Add a bash code to detect extension and update output file name * 👌 IMPROVE: clean code Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2021-09-27 15:14:35 +00:00
- name: lima test_lima_bam
command: nextflow run tests/modules/lima -entry test_lima_bam -c tests/config/nextflow.config
tags:
- lima
files:
- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam
md5sum: 14b51d7f44e30c05a5b14e431a992097
- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi
md5sum: 6ae7f057304ad17dd9d5f565d72d3f7b
- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.consensusreadset.xml
contains: [ 'ConsensusReadSet' ]
- path: output/lima/test.fl.json
contains: [ 'ConsensusReadSet' ]
- path: output/lima/test.fl.lima.clips
md5sum: fa03bc75bd78b2648a139fd67c69208f
- path: output/lima/test.fl.lima.counts
md5sum: 842c6a23ca2de504ced4538ad5111da1
- path: output/lima/test.fl.lima.guess
md5sum: d3675af3ca8a908ee9e3c231668392d3
- path: output/lima/test.fl.lima.report
md5sum: dc073985322ae0a003ccc7e0fa4db5e6
- path: output/lima/test.fl.lima.summary
md5sum: bcbcaaaca418bdeb91141c81715ca420
- name: lima test_lima_fa
command: nextflow run tests/modules/lima -entry test_lima_fa -c tests/config/nextflow.config
tags:
- lima
files:
- path: output/lima/test.fl.lima.clips
md5sum: 1012bc8874a14836f291bac48e8482a4
- path: output/lima/test.fl.lima.counts
md5sum: a4ceaa408be334eaa711577e95f8730e
- path: output/lima/test.fl.lima.guess
md5sum: 651e5f2b438b8ceadb3e06a2177e1818
- path: output/lima/test.fl.lima.report
md5sum: bd4a8bde17471563cf91aab4c787911d
- path: output/lima/test.fl.lima.summary
md5sum: 03be2311ba4afb878d8e547ab38c11eb
- name: lima test_lima_fa_gz
command: nextflow run tests/modules/lima -entry test_lima_fa_gz -c tests/config/nextflow.config
tags:
- lima
files:
- path: output/lima/test.fl.lima.clips
md5sum: 1012bc8874a14836f291bac48e8482a4
- path: output/lima/test.fl.lima.counts
md5sum: a4ceaa408be334eaa711577e95f8730e
- path: output/lima/test.fl.lima.guess
md5sum: 651e5f2b438b8ceadb3e06a2177e1818
- path: output/lima/test.fl.lima.report
md5sum: bd4a8bde17471563cf91aab4c787911d
- path: output/lima/test.fl.lima.summary
md5sum: 03be2311ba4afb878d8e547ab38c11eb
- name: lima test_lima_fq
command: nextflow run tests/modules/lima -entry test_lima_fq -c tests/config/nextflow.config
tags:
- lima
files:
- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq
md5sum: ef395f689c5566f501e300bb83d7a5f2
- path: output/lima/test.fl.lima.clips
md5sum: 5c16ef8122f6f1798acc30eb8a30828c
- path: output/lima/test.fl.lima.counts
md5sum: 767b687e6eda7b24cd0e577f527eb2f0
- path: output/lima/test.fl.lima.guess
md5sum: 31b988aab6bda84867e704b9edd8a763
- path: output/lima/test.fl.lima.report
md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd
- path: output/lima/test.fl.lima.summary
md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
- name: lima test_lima_fq_gz
command: nextflow run tests/modules/lima -entry test_lima_fq_gz -c tests/config/nextflow.config
tags:
- lima
files:
- path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.fastq.gz
md5sum: 32c11db85f69a1b4454b6bbd794b6df2
- path: output/lima/test.fl.lima.clips
md5sum: 5c16ef8122f6f1798acc30eb8a30828c
- path: output/lima/test.fl.lima.counts
md5sum: 767b687e6eda7b24cd0e577f527eb2f0
- path: output/lima/test.fl.lima.guess
md5sum: 31b988aab6bda84867e704b9edd8a763
- path: output/lima/test.fl.lima.report
md5sum: ad2a9b1eeb4cda4a1f69ef4b7520b5fd
- path: output/lima/test.fl.lima.summary
md5sum: e91d3c386aaf4effa63f33ee2eb7da2a
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