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Add helptest to nextflow_schema,add versions to longread_preprocessing

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Sofia Stamouli 2022-10-25 11:13:26 +02:00
parent d3d4297ca9
commit 8c3e80b6ea
4 changed files with 6 additions and 3 deletions
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1
.github/workflows/ci.yml vendored
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@ -23,7 +23,6 @@ jobs:
- "21.10.3" - "21.10.3"
- "latest-everything" - "latest-everything"
parameters: parameters:
- "--preprocessing_qc_tool fastqc"
- "--preprocessing_qc_tool falco" - "--preprocessing_qc_tool falco"
- "--perform_longread_qc false" - "--perform_longread_qc false"
- "--perform_shortread_qc false" - "--perform_shortread_qc false"

2
docs/usage.md
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@ -168,7 +168,7 @@ work # Directory containing the nextflow working files
### Sequencing quality control ### Sequencing quality control
nf-core taxprofiler offers [`Falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). nf-core taxprofiler offers [`falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
### Preprocessing Steps ### Preprocessing Steps

4
nextflow_schema.json
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@ -712,7 +712,9 @@
"preprocessing_qc_tool": { "preprocessing_qc_tool": {
"type": "string", "type": "string",
"default": "fastqc", "default": "fastqc",
"enum": ["fastqc", "falco"] "enum": ["fastqc", "falco"],
"help_text": "Falco is aimed at being a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
"description": "By default, the pipeline utilizes FastQC tool for quality control of raw sequencing reads"
} }
} }
} }

2
subworkflows/local/longread_preprocessing.nf
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@ -56,10 +56,12 @@ workflow LONGREAD_PREPROCESSING {
if (params.preprocessing_qc_tool == 'fastqc') { if (params.preprocessing_qc_tool == 'fastqc') {
FASTQC_PROCESSED ( ch_processed_reads ) FASTQC_PROCESSED ( ch_processed_reads )
ch_versions = ch_versions.mix( FASTQC_PROCESSED.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip ) ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
} else if (params.preprocessing_qc_tool == 'falco') { } else if (params.preprocessing_qc_tool == 'falco') {
FALCO_PROCESSED ( ch_processed_reads ) FALCO_PROCESSED ( ch_processed_reads )
ch_versions = ch_versions.mix( FALCO_PROCESSED.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt ) ch_multiqc_files = ch_multiqc_files.mix( FALCO_PROCESSED.out.txt )
} }