Updating workflow files to work with Igenome #388
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -43,18 +43,21 @@ workflow NFCORE_SMRNASEQ { | |
| take: | ||
| ch_input // channel: samplesheet file as specified to --input | ||
| ch_samplesheet // channel: sample fastqs parsed from --input | ||
| fasta // params.fasta | ||
| mirtrace_species // params.mirtrace_species | ||
| bowtie_index // params.bowtie_index | ||
| ch_versions // channel: [ path(versions.yml) ] | ||
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| main: | ||
| //Config checks | ||
| // Check optional parameters | ||
| if (!params.mirgenedb && !mirtrace_species) { | ||
| exit 1, "Reference species for miRTrace is not defined via the --mirtrace_species parameter." | ||
| } | ||
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| // Genome options | ||
| mirna_gtf_from_species = mirtrace_species ? (mirtrace_species == 'hsa' ? "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hsa.gff3" : "https://mirbase.org/download/CURRENT/genomes/${mirtrace_species}.gff3") : false | ||
| mirna_gtf = params.mirna_gtf ?: mirna_gtf_from_species | ||
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| if (!params.mirgenedb) { | ||
| if (params.mature) { reference_mature = file(params.mature, checkIfExists: true) } else { exit 1, "Mature miRNA fasta file not found: ${params.mature}" } | ||
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@@ -108,12 +111,12 @@ workflow NFCORE_SMRNASEQ { | |
| ) | ||
| ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions) | ||
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| ch_fasta = fasta ? file(fasta): [] | ||
| ch_reads_for_mirna = FASTQ_FASTQC_UMITOOLS_FASTP.out.reads | ||
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| // even if bowtie index is specified, there still needs to be a fasta. | ||
| // without fasta, no genome analysis. | ||
| if(fasta) { | ||
|
There was a problem hiding this comment. Perhaps since we are changing this for all fasta, we could adhere to adding the ch_ prefix: https://nf-co.re/docs/guidelines/components/subworkflows If this breaks things or you think it is too complicated we can open a new issue and address it separately. There was a problem hiding this comment. I originally tackled this issue by converting value variables to value channels, and converting file string variables to path channels, but it created a lot of issues downstream. I want to tackle the conversion of all of these variables into channels in #390. To make sure that these are the only changes implemented in the branch There was a problem hiding this comment. this fasta variable is just equal to params.fasta, so I will convert it to val_fasta |
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| //Prepare bowtie index, unless specified | ||
| //This needs to be done here as the index is used by GENOME_QUANT | ||
| if(params.bowtie_index) { | ||
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@@ -124,7 +127,7 @@ workflow NFCORE_SMRNASEQ { | |
| } else { | ||
| Channel.fromPath("${params.bowtie_index}**ebwt", checkIfExists: true).ifEmpty{ error "Bowtie1 index directory not found: ${params.bowtie_index}" }.filter { it != null }.set { ch_bowtie_index } | ||
| } | ||
| } else { | ||
| INDEX_GENOME ( [ [:], ch_fasta ] ) | ||
| ch_versions = ch_versions.mix(INDEX_GENOME.out.versions) | ||
| ch_bowtie_index = INDEX_GENOME.out.index | ||
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@@ -181,8 +184,8 @@ workflow NFCORE_SMRNASEQ { | |
| // | ||
| // SUBWORKFLOW: MIRTRACE | ||
| // | ||
| if (mirtrace_species) { | ||
|
There was a problem hiding this comment. same comment as before, perhaps adding |
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| MIRTRACE(ch_mirtrace_inputs, mirtrace_species) | ||
| ch_versions = ch_versions.mix(MIRTRACE.out.versions) | ||
| } else { | ||
| log.warn "The parameter --mirtrace_species is absent. MIRTRACE quantification skipped." | ||
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@@ -209,20 +212,21 @@ workflow NFCORE_SMRNASEQ { | |
| ch_reads_for_mirna = CONTAMINANT_FILTER.out.filtered_reads | ||
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| } | ||
| //MIRNA_QUANT process should still run even if mirtrace_species is null when mirgendb is true | ||
| MIRNA_QUANT ( | ||
| [ [:], reference_mature], | ||
| [ [:], reference_hairpin], | ||
| mirna_gtf, | ||
| ch_reads_for_mirna, | ||
| mirtrace_species | ||
| ) | ||
| ch_versions = ch_versions.mix(MIRNA_QUANT.out.versions) | ||
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| // | ||
| // GENOME | ||
| // | ||
| genome_stats = Channel.empty() | ||
| if (fasta){ | ||
| GENOME_QUANT ( ch_bowtie_index, ch_fasta, MIRNA_QUANT.out.unmapped ) | ||
| genome_stats = GENOME_QUANT.out.stats | ||
| ch_versions = ch_versions.mix(GENOME_QUANT.out.versions) | ||
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@@ -306,7 +310,7 @@ workflow NFCORE_SMRNASEQ { | |
| ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.mature_stats.collect({it[1]}).ifEmpty([])) | ||
| ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.hairpin_stats.collect({it[1]}).ifEmpty([])) | ||
| ch_multiqc_files = ch_multiqc_files.mix(MIRNA_QUANT.out.mirtop_logs.collect().ifEmpty([])) | ||
| if (mirtrace_species) { | ||
| ch_multiqc_files = ch_multiqc_files.mix(MIRTRACE.out.results.collect().ifEmpty([])) | ||
| } | ||
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Interesting. I thought these had to be defined in the
PIPELINE_INITIALISATIONand the outputs fromPIPELINE_INITIALISATIONhave to be passed to the main workflow. See:https://github.com/nf-core/taxprofiler/blob/5d3ee5513a84f92773c8376c55b5f4da39835307/main.nf#L74-L91
or
https://github.com/nf-core/phaseimpute/blob/f2823b024800155cd87d70f406794324c4123dfd/main.nf#L140-L151
but I see sarek and rnaseq have different approaches as well.
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I'll leave it as it is, as we discussed, since there doesn't seem to be a standard for how to set up the new template, we can always change it later if we have a reason to do so