update Simpleaf modules, subworkflow #424
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@@ -28,6 +28,8 @@ process MTX_TO_H5AD { | |
| script: | ||
| def aligner = (input_aligner in [ 'cellranger', 'cellrangerarc', 'cellrangermulti' ]) ? 'cellranger' : input_aligner | ||
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| aligner = input_aligner == "alevin" ? "simpleaf" : aligner | ||
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There was a problem hiding this comment. Is this for backwards compatibility? I'm afraid one needs to fix it at multiple locations otherwise. There was a problem hiding this comment. I renamed the file instead. Now the python script file is called However, thanks for pointing this out. I will do some updates to ensure backward compatibility. One related thing is, I am struggling with the documentation. There are a few confusions:
So, I am thinking of replacing "alevin" and "salmon" with "simpleaf" everywhere in the workflow, including file&folder names. This will avoid all confusions, but will change the file structure and the default "aligner" option. What do you think? |
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| template "mtx_to_h5ad_${aligner}.py" | ||
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| stub: | ||
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| /* -- IMPORT LOCAL MODULES/SUBWORKFLOWS -- */ | ||
| include { ALEVINQC } from '../../modules/local/alevinqc' | ||
| include { SIMPLEAF_INDEX } from '../../../modules/modules/nf-core/simpleaf/index' | ||
| include { SIMPLEAF_QUANT } from '../../../modules/modules/nf-core/simpleaf/quant' | ||
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| workflow SCRNASEQ_SIMPLEAF { | ||
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| take: | ||
| ch_genome_fasta // channel | ||
| ch_genome_gtf // channel | ||
| transcript_fasta | ||
| simpleaf_index | ||
| txp2gene | ||
| barcode_whitelist | ||
| chemistry | ||
| resolution | ||
| ch_fastq // channel | ||
| map_dir | ||
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There was a problem hiding this comment. I am preparing moving this subworkflow to nf-core/modules. simpleaf quant can take a folder that contains mapping results to skip indexing and mapping and directly jump into quantification. this |
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| main: | ||
| ch_versions = Channel.empty() | ||
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| /* | ||
| * Build salmon index | ||
| */ | ||
| if ( !simpleaf_index || !map_dir ) { | ||
| // define input channels for index building | ||
| // we can either use the genome fasta and gtf files or the transcript fasta file | ||
| if ( transcript_fasta ) { | ||
| ch_genome_fasta_gtf = [ [:],[],[] ] | ||
| ch_transcript_fasta = Channel.of( [ [id: "${transcript_fasta.getBaseName()}"], transcript_fasta ] ) | ||
| } else { | ||
| ch_genome_fasta_gtf = ch_genome_fasta.combine( ch_genome_gtf ).map{ fasta, gtf -> [[id: "${fasta.getBaseName()}"], fasta, gtf] } | ||
| ch_transcript_fasta = Channel.of( [ [:], [] ] ) | ||
| } | ||
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| SIMPLEAF_INDEX( | ||
| ch_genome_fasta_gtf, | ||
| ch_transcript_fasta | ||
| ) | ||
| // Channel of tuple(meta, index dir) | ||
| simpleaf_index = SIMPLEAF_INDEX.out.index.collect() | ||
| // Channel of t2g path or empty | ||
| t2g = SIMPLEAF_INDEX.out.t2g.collect() | ||
| ch_versions = ch_versions.mix(SIMPLEAF_INDEX.out.versions) | ||
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| // ensure txp2gene is a Channel | ||
| if (!txp2gene) { | ||
| txp2gene = t2g | ||
| } else { | ||
| txp2gene = Channel.of( txp2gene ) | ||
| } | ||
| } else { | ||
| // ensure simpleaf index and txp2gene are Channels | ||
| simpleaf_index = Channel.of( [ [:], simpleaf_index ] ) | ||
| txp2gene = Channel.of( txp2gene ) | ||
| } | ||
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| // define input channels for quantification | ||
| // we can either use the mapping results or the reads and index files | ||
| if ( map_dir ) { | ||
| ch_chemistry_reads = Channel.of( [ [:],[],[] ] ) | ||
| ch_index_t2g = Channel.of( [ [:],[],[] ] ) | ||
| ch_map_dir = Channel.of( [ [id: map_dir.baseName], map_dir ] ) | ||
| } else { | ||
| ch_chemistry_reads = ch_fastq.map{ meta, files -> tuple(meta + ["chemistry": chemistry], chemistry, files) } | ||
| ch_index_t2g = simpleaf_index.combine( txp2gene ) | ||
| ch_map_dir = [ [:],[] ] | ||
| } | ||
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| /* | ||
| * Perform quantification with salmon alevin | ||
| */ | ||
| SIMPLEAF_QUANT ( | ||
| ch_chemistry_reads, | ||
| ch_index_t2g, | ||
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There was a problem hiding this comment. Could it be that a There was a problem hiding this comment.
Could you point out which line you referred to?
I was just making everything as channel for consistency. Keeping them as values sound good. |
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| [[:], "unfiltered-pl", [], barcode_whitelist ], | ||
| resolution, | ||
| ch_map_dir | ||
| ) | ||
| ch_versions = ch_versions.mix(SIMPLEAF_QUANT.out.versions) | ||
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| ch_af_map = map_dir ? ch_map_dir : SIMPLEAF_QUANT.out.map | ||
| /* | ||
| * Run alevinQC | ||
| */ | ||
| ALEVINQC( SIMPLEAF_QUANT.out.quant, SIMPLEAF_QUANT.out.quant, ch_af_map ) | ||
| ch_versions = ch_versions.mix(ALEVINQC.out.versions) | ||
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| emit: | ||
| ch_versions | ||
| txp2gene | ||
| index = simpleaf_index | ||
| map = SIMPLEAF_QUANT.out.map | ||
| quant = SIMPLEAF_QUANT.out.quant | ||
| alevinqc = ALEVINQC.out.report | ||
| } | ||
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this should probably not be there
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removed!