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57 changes: 34 additions & 23 deletions
57
subworkflows/local/generate_downstream_samplesheets/main.nf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,54 @@ | ||
| // | ||
| // Subworkflow with functionality specific to the nf-core/taxprofiler pipeline | ||
| // Subworkflow with functionality specific to the nf-core/mag pipeline | ||
| // | ||
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| workflow GENERATE_DOWNSTREAM_SAMPLESHEETS { | ||
| workflow SAMPLESHEET_MAG { | ||
| take: | ||
| ch_processed_reads | ||
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| main: | ||
| format = 'csv' // most common format in nf-core | ||
| format_sep = ',' | ||
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| if ( params.generate_pipeline_samplesheets == 'mag' && params.save_analysis_ready_fastqs ) { | ||
| def fastq_rel_path = '/' | ||
| format = 'csv' | ||
| format_sep = ',' | ||
| ch_list_for_samplesheet = ch_processed_reads | ||
| .filter { meta, sample_id, instrument_platform,fastq_1,fastq_2,fasta -> (fastq_1 && fastq_2) && !fasta } | ||
| .map { | ||
| meta, sample_id, instrument_platform,fastq_1,fastq_2,fasta -> | ||
| def sample = meta.id | ||
| def run = meta.run_accession //this should be optional | ||
| def group = "" | ||
| def short_reads_1 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_1.getName() | ||
| def short_reads_2 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_2.getName() | ||
| def long_reads = "" | ||
| [sample: sample, run: run, group: group, short_reads_1: short_reads_1, short_reads_2: short_reads_2, long_reads: long_reads] | ||
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| ch_list_for_samplesheet = ch_processed_reads | ||
| .filter { meta, sample_id, instrument_platform,fastq_1,fastq_2,fasta -> (fastq_1 && fastq_2) && !fasta }.view() | ||
| .map { | ||
| meta, sample_id, instrument_platform,fastq_1,fastq_2,fasta -> | ||
| def sample = meta.id | ||
| def run = meta.run_accession //this should be optional | ||
| def group = "" | ||
| def short_reads_1 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_1.getName() | ||
| def short_reads_2 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_2.getName() | ||
| def long_reads = "" | ||
| [sample: sample, run: run, group: group, short_reads_1: short_reads_1, short_reads_2: short_reads_2, long_reads: long_reads] | ||
| } | ||
| .tap{ ch_header } | ||
| } | ||
| .tap { ch_colnames } | ||
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| channelToSamplesheet(ch_colnames, ch_list_for_samplesheet, 'downstream_samplesheets', format, format_sep) | ||
| } | ||
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| workflow GENERATE_DOWNSTREAM_SAMPLESHEETS { | ||
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| take: | ||
| ch_processed_reads | ||
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| main: | ||
| if ( params.generate_pipeline_samplesheets == 'mag' && params.save_analysis_ready_fastqs ) { | ||
| SAMPLESHEET_MAG(ch_processed_reads) | ||
| } | ||
| } | ||
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| def channelToSamplesheet(ch_header, ch_list_for_samplesheet, outdir_subdir, format, format_sep) { | ||
| // Constructs the header string and then the strings of each row, and | ||
| // finally concatenates for saving. Originally designed by @mahesh-panchal | ||
| ch_header | ||
| .first() | ||
| .map{ it.keySet().join(format_sep) } | ||
| .concat( ch_list_for_samplesheet.map{ it.values().join(format_sep) }) | ||
| .map { it.keySet().join(format_sep) } | ||
| .concat(ch_list_for_samplesheet.map { it.values().join(format_sep) }) | ||
| .collectFile( | ||
| name:"${params.outdir}/downstream_samplesheet/${params.generate_pipeline_samplesheets}.${format}", | ||
| name: "${params.outdir}/${outdir_subdir}/${params.generate_pipeline_samplesheets}.${format}", | ||
| newLine: true, | ||
| sort: false | ||
| ) | ||
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| } |