kfukuta/wf-transcriptomes-v202
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Skip fastq>a conversion

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This commit is contained in:
Chris Wright 2022-07-14 09:08:44 +00:00
parent 3efcf30a34
commit 1ab5e2744c
3 changed files with 7 additions and 4 deletions
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4
CHANGELOG.md
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@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [unreleased]
### Changed
- Skip unnecessary conversion to fasta from fastq.
## [v0.1.4] ## [v0.1.4]
### Changed ### Changed
- Args parser for fastqingress - Args parser for fastqingress

2
nextflow_schema.json
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@ -15,7 +15,7 @@
"out_dir": { "out_dir": {
"type": "string", "type": "string",
"default": "output", "default": "output",
"format": "path", "format": "directory-path",
"description": "Directory for output of all user-facing files." "description": "Directory for output of all user-facing files."
}, },
"fastq": { "fastq": {

3
reference_assembly.nf
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@ -20,8 +20,7 @@ process map_reads{
RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}", RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}",
Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """ Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """
""" """
seqkit fq2fa ${fastq_reads} -o "reads.fa"; minimap2 -t ${params.threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
minimap2 -t ${params.threads} -ax splice ${params.minimap2_opts} ${index} "reads.fa"\
| samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\ | samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\
| seqkit bam -j ${params.threads} -x -T '${ContextFilter}' -\ | seqkit bam -j ${params.threads} -x -T '${ContextFilter}' -\
| samtools sort -@ ${params.threads} -o "${sample_id}_reads_aln_sorted.bam" - ; | samtools sort -@ ${params.threads} -o "${sample_id}_reads_aln_sorted.bam" - ;