mirror of
https://github.com/MillironX/nf-core_modules.git
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4ec8b025bd
* 📦 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>
77 lines
2.2 KiB
YAML
77 lines
2.2 KiB
YAML
name: lima
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description: lima - The PacBio Barcode Demultiplexer and Primer Remover
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keywords:
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- sort
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tools:
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- lima:
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description: lima - The PacBio Barcode Demultiplexer and Primer Remover
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homepage: https://github.com/PacificBiosciences/pbbioconda
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documentation: https://lima.how/
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tool_dev_url: https://github.com/pacificbiosciences/barcoding/
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doi: ""
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licence: ['BSD-3-clause-Clear']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- ccs:
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type: file
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description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs
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pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}"
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- primers:
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type: file
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description: Fasta file, sequences of primers
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pattern: "*.fasta"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- bam:
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type: file
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description: A bam file of ccs purged of primers
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pattern: "*.bam"
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- pbi:
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type: file
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description: Pacbio index file of ccs purged of primers
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pattern: "*.bam"
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- xml:
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type: file
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description: An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads.
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pattern: "*.xml"
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- json:
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type: file
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description: A metadata json file
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pattern: "*.json"
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- clips:
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type: file
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description: A fasta file of clipped primers
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pattern: "*.clips"
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- counts:
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type: file
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description: A tabulated file of describing pairs of primers
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pattern: "*.counts"
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- guess:
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type: file
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description: A second tabulated file of describing pairs of primers (no doc available)
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pattern: "*.guess"
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- report:
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type: file
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description: A tab-separated file about each ZMW, unfiltered
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pattern: "*.report"
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- summary:
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type: file
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description: This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered.
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pattern: "*.summary"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@sguizard"
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