update Simpleaf modules, subworkflow #424
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.1.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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| tag "$meta.id" | ||
| label 'process_low' | ||
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| //The alevinqc 1.14.0 container is broken, missing some libraries - thus reverting this to previous 1.12.1 version | ||
| conda "bioconda::bioconductor-alevinqc=1.12.1" |
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Ideally, this would also be a module on nf-core/modules. But if you don't have time right now, we can also address this at a later point.
| @@ -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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Is this for backwards compatibility?
Can't we fix this at an earlier point in the pipeline, i.e. at the very beginning set aligner to simpleaf if it's alevin and then use simpleaf throughout the pipeline?
I'm afraid one needs to fix it at multiple locations otherwise.
| barcode_whitelist = null | ||
| salmon_index = null | ||
| simpleaf_umi_resolution = "cr-like" |
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What does this parameter do? Is this a reasonable default, or should it be set based on the protocol used? We have a protocols.json file somewhere that already sets other parameters based on the protocol.
| chemistry | ||
| resolution | ||
| ch_fastq // channel | ||
| map_dir |
| ch_h5ads.filter { meta, mtx_files -> meta.input_type == 'raw' } | ||
| ch_h5ads | ||
| .filter { meta, mtx_files -> meta.input_type == 'raw' } | ||
| .map { meta, mtx_files -> [ meta + [input_type: 'filtered'], mtx_files ]} // to avoid name collision |
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Why do you filter to raw and then set the input_type to filtered?
| */ | ||
| SIMPLEAF_QUANT ( | ||
| ch_chemistry_reads, | ||
| ch_index_t2g, |
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Could it be that a .collect() is needed here? Alternativley, maybe it could be avoided to build FIFO channels above by not using Channel.of at all and just keep everything as values.
Reopen #361 after updating simpleaf central modules. See this PR. I have tested using a 10x 500 dataset. Once the modules' PR is merged, we can start merging this PR
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).