Initial commit to add fq lint module #1453
Conversation
There was a problem hiding this comment.
In general, this will be a great contribution!
But any 'nf-core' components (modules, subworkflows) need to be updated in the modules repo first (e.g. here). Then we can use the nf-core tooling to update those components in the subworkflow.
It would also be good to capture the outputs. So the subworkflow should have an output channel for the linting report, and we should set a publishing rule to place the output in the output directory. I can help with that when we get there.
| @@ -4,6 +4,7 @@ include { BBMAP_BBSPLIT } from '../../../modules/nf-core/bbmap | |||
| include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main' | |||
| include { SORTMERNA } from '../../../modules/nf-core/sortmerna/main' | |||
| include { SORTMERNA as SORTMERNA_INDEX } from '../../../modules/nf-core/sortmerna/main' | |||
| include { FQ_LINT } from '../../../modules/nf-core/fq/lint/main' | |||
There was a problem hiding this comment.
I see this change has not been made on nf-core/modules- it needs to be done there, and then the component added here
| ch_reads | ||
| .map { | ||
| meta, fastqs -> | ||
| return [meta, fastqs.flatten()] | ||
| } | ||
| .set { ch_fastq_lint } | ||
|
|
||
| // | ||
| // MODULE: Lint FastQ files | ||
| // | ||
| if (!skip_linting) { | ||
| FQ_LINT ( | ||
| ch_fastq_lint | ||
| ) | ||
| ch_versions = ch_versions.mix(FQ_LINT.out.versions.first()) | ||
| } |
There was a problem hiding this comment.
| ch_reads | |
| .map { | |
| meta, fastqs -> | |
| return [meta, fastqs.flatten()] | |
| } | |
| .set { ch_fastq_lint } | |
| // | |
| // MODULE: Lint FastQ files | |
| // | |
| if (!skip_linting) { | |
| FQ_LINT ( | |
| ch_fastq_lint | |
| ) | |
| ch_versions = ch_versions.mix(FQ_LINT.out.versions.first()) | |
| } | |
| // | |
| // MODULE: Lint FastQ files | |
| // | |
| if (!skip_linting) { | |
| FQ_LINT ( | |
| ch_fastq_lint.map{ meta, fastqs -> [meta, fastqs.flatten()] } | |
| ) | |
| ch_versions = ch_versions.mix(FQ_LINT.out.versions.first()) | |
| } |
(but again, this needs PR'ing to the modules repo first)
There was a problem hiding this comment.
Also, the linting outputs should be added as a subworkflow output
There was a problem hiding this comment.
Thanks so much for reviewing @pinin4fjords ! I opened a PR in the modules repo here: nf-core/modules#7000
|
Apologies, I ended up repeating this in #1461 after I'd improved the subworkflow (I had to do quite a bit of work on the testing suite). But I'll be sure to credit you in the next release. |
Addition to the RNA-seq pipeline to include the fq lint module and validate single-end or paired-end FastQ files. This will prevent the pipeline from continuing and running more computationally-heavy steps on corrupted FastQ files, and will address open issue #1281 .
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).