Add fq2bam fq align dd bwamem #9309
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…dules into add_fq2bam_fq_align_dd_bwamem
…dules into add_fq2bam_fq_align_dd_bwamem
Removed and added to specific subworkflow tests directives! |
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Shouldn't touch this file, undo any edits here please
| run("BWA_INDEX") { | ||
| script "../../../../modules/nf-core/bwa/index/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
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| run("BWA_INDEX", alias: 'BWA_INDEX_PE') { | ||
| script "../../../../modules/nf-core/bwa/index/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test' ], // meta map | ||
| file('https://github.com/nf-core/test-datasets/raw/methylseq/reference/genome.fa', checkIfExists: true) | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
| } |
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If it's the same genome why do we need to run the same indexing twice? We can just have a single global setup.
| params { | ||
| use_gpu = true | ||
| bwa_prefix = 'genome.fa' | ||
| } |
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Why did you include this? It shouldn't be necessary for the subworkflow, everything is passed as an input. Best to keep it as simple as possible, remove it everywhere
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Aah, now I see. You got your inspiration from the parabricks/fq2bam module. You can do this but then also need to update the config file, to parse these params in the correct variables.
Given the amount of arguments that there already are in the nextflow.config file, I would just delete this param section.
| } | ||
| } | ||
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| test("Params: parabricks/fq2bam single-end | use_gpu ") { |
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This doesn't follow nf-core naming convetion guidelines .
Please also update all other test names
| test("Params: parabricks/fq2bam single-end | use_gpu ") { | |
| test("Sarscov2 fasta - SE - deduplicate- with GPU ") { | |
| input[4] = false // skip_deduplication | ||
| input[5] = true // use_gpu | ||
| input[6] = Channel.empty() // interval_file | ||
| input[7] = Channel.empty() // known_sites |
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Please align these comments .
| tag "gpu" | ||
| tag "subworkflows" | ||
| tag "subworkflows_nfcore" | ||
| tag "subworkflows/fastq_align_dedup_bwamem" | ||
| tag "parabricks/fq2bam" | ||
| tag "samtools/index" | ||
| tag "picard/markduplicates" | ||
| tag "untar" |
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Think you are missing a few in here, mostly all the samtools ones.
| tag "gpu" | ||
| tag "subworkflows" | ||
| tag "subworkflows_nfcore" | ||
| tag "subworkflows/fastq_align_dedup_bwamem" | ||
| tag "parabricks/fq2bam" | ||
| tag "samtools/index" | ||
| tag "picard/markduplicates" | ||
| tag "untar" |
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Maybe i missed it, where are you using untar?
| { assert snapshot( | ||
| workflow.out.bam.collect { meta, bamfile -> bam(bamfile).getReadsMD5() }, | ||
| workflow.out.bai.collect { meta, bai -> file(bai).name }, | ||
| workflow.out.samtools_flagstat, | ||
| workflow.out.samtools_stats, | ||
| workflow.out.samtools_index_stats, | ||
| workflow.out.picard_metrics.collect { meta, metrics -> file(metrics).name }, | ||
| workflow.out.multiqc.flatten().collect { path -> file(path).name }, | ||
| workflow.out.versions | ||
| ).match() } |
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This is the stub run, we can just leave it as is.
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(workflow.out).match() } | ||
| ) |
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| assertAll( | |
| { assert workflow.success }, | |
| { assert snapshot(workflow.out).match() } | |
| ) | |
| assertAll( | |
| { assert workflow.success }, | |
| { assert snapshot( | |
| workflow.out, | |
| workflow.out.versions.collect{ path(it).yaml } | |
| ).match() } | |
| ) | |
| @@ -0,0 +1,160 @@ | |||
| { | |||
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Yeah none of the tests seems to have ran.
PR checklist
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda