Add support for generating taxprofiler/funcscan input samplesheets for preprocessed FASTQs/FASTAs #688
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Contributor
There was a problem hiding this comment. It looks like @jfy133 used only one workflow, which will selectively generate samplesheets based on params.generate_pipeline_samplesheets. Do you think it would be best to keep that consistent?
Contributor
There was a problem hiding this comment. Also, since FastQ files are being pulled from the publishDir, it might be a good idea to include options that override user inputs for params.publish_dir_mode (so that it is always 'copy' if a samplesheet is generated) and params.save_clipped_reads, params.save_phixremoved_reads ...etc so that the preprocessed FastQ files are published to the params.outdir if a downstream samplesheet is generated |
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| // | ||
| // Subworkflow with functionality specific to the nf-core/mag pipeline | ||
| // | ||
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| workflow SAMPLESHEET_TAXPROFILER { | ||
| take: | ||
| ch_reads | ||
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| main: | ||
| def fastq_rel_path = '/' | ||
| if (params.bbnorm) { | ||
| fastq_rel_path = '/bbmap/bbnorm/' | ||
| } else if (!params.keep_phix) { | ||
| fastq_rel_path = '/QC_shortreads/remove_phix/' | ||
| } | ||
| else if (params.host_fasta) { | ||
| fastq_rel_path = '/QC_shortreads/remove_host/' | ||
| } | ||
| else if (!params.skip_clipping) { | ||
| fastq_rel_path = '/QC_shortreads/fastp/' | ||
| } | ||
| ch_list_for_samplesheet = ch_reads | ||
| .map { | ||
| meta, fastq -> | ||
| def sample = meta.id | ||
| def run_accession = meta.id | ||
| def instrument_platform = "" | ||
| def fastq_1 = file(params.outdir).toString() + fastq_rel_path + meta.id + '/' + fastq[0].getName() | ||
| def fastq_2 = file(params.outdir).toString() + fastq_rel_path + meta.id + '/' + fastq[1].getName() | ||
| def fasta = "" | ||
| [ sample: sample, run_accession: run_accession, instrument_platform: instrument_platform, fastq_1: fastq_1, fastq_2: fastq_2, fasta: fasta ] | ||
| } | ||
| .tap{ ch_header } | ||
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| ch_header | ||
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jfy133 marked this conversation as resolved.
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| .first() | ||
| .map{ it.keySet().join(",") } | ||
| .concat( ch_list_for_samplesheet.map{ it.values().join(",") }) | ||
| .collectFile( | ||
| name:"${params.outdir}/downstream_samplesheet/taxprofiler.csv", | ||
| newLine: true, | ||
| sort: false | ||
| ) | ||
| } | ||
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| workflow SAMPLESHEET_FUNCSCAN { | ||
| take: | ||
| ch_assemblies | ||
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| main: | ||
| ch_list_for_samplesheet = ch_assemblies | ||
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Member
There was a problem hiding this comment. Next thing which I don't think will be so complicated is to add another input channel for bins, and here make an if/else statement if they want to send just the raw assemblies (all contigs) or binned contigs to the samplesheet. It will need another pipeline level parameter too though |
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| .map { | ||
| meta, filename -> | ||
| def sample = meta.id | ||
| def fasta = file(params.outdir).toString() + '/Assembly/' + meta.assembler + '/' + filename.getName() | ||
| [ sample: sample, fasta: fasta ] | ||
| } | ||
| .tap{ ch_header } | ||
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| ch_header | ||
| .first() | ||
| .map{ it.keySet().join(",") } | ||
| .concat( ch_list_for_samplesheet.map{ it.values().join(",") }) | ||
| .collectFile( | ||
| name:"${params.outdir}/downstream_samplesheet/funcscan.csv", | ||
| newLine: true, | ||
| sort: false | ||
| ) | ||
| } | ||
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| workflow GENERATE_DOWNSTREAM_SAMPLESHEETS { | ||
| take: | ||
| ch_reads | ||
| ch_assemblies | ||
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| main: | ||
| def downstreampipeline_names = params.generate_pipeline_samplesheets.split(",") | ||
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Member
There was a problem hiding this comment. I've also implemented the same system in createtaxdb now, but with an additional input validation thing that you should also adopt here (i.e., to check that someone doesn't add an unsupported pipeline, or makes a typo). Check the |
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| if ( downstreampipeline_names.contains('taxprofiler') && params.save_clipped_reads ) { // save_clipped_reads must be true | ||
| SAMPLESHEET_TAXPROFILER(ch_reads) | ||
| } | ||
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| if ( downstreampipeline_names.contains('funcscan') ) { | ||
| SAMPLESHEET_FUNCSCAN(ch_assemblies) | ||
| } | ||
| } | ||
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