Delete lib directory and replace with utils_* subworkflows #1197
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Just please not that there is still an issue with the monochrome_logs params: |
Yep, I think this is actually coming from the nf-validation plugin because I see the same issue with nf-core/fetchngs. Can you create an issue there please? I started trying to look at the nf-validation code base to find the issue but got distracted. |
adamrtalbot
reviewed
Jan 22, 2024
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| workflow PREPARE_GENOME { | ||
| take: | ||
| fasta // file: /path/to/genome.fasta | ||
| gtf // file: /path/to/genome.gtf | ||
| gff // file: /path/to/genome.gff | ||
| additional_fasta // file: /path/to/additional.fasta | ||
| transcript_fasta // file: /path/to/transcript.fasta | ||
| gene_bed // file: /path/to/gene.bed | ||
| splicesites // file: /path/to/splicesites.txt | ||
| bbsplit_fasta_list // file: /path/to/bbsplit_fasta_list.txt | ||
| star_index // directory: /path/to/star/index/ | ||
| rsem_index // directory: /path/to/rsem/index/ | ||
| salmon_index // directory: /path/to/salmon/index/ | ||
| kallisto_index // directory: /path/to/kallisto/index/ | ||
| hisat2_index // directory: /path/to/hisat2/index/ | ||
| bbsplit_index // directory: /path/to/rsem/index/ | ||
| gencode // boolean: whether the genome is from GENCODE | ||
| is_aws_igenome // boolean: whether the genome files are from AWS iGenomes | ||
| biotype // string: if additional fasta file is provided biotype value to use when appending entries to GTF file | ||
| prepare_tool_indices // list: tools to prepare indices for | ||
| filter_gtf // boolean: whether to filter GTF file | ||
| fasta // file: /path/to/genome.fasta | ||
| gtf // file: /path/to/genome.gtf | ||
| gff // file: /path/to/genome.gff | ||
| additional_fasta // file: /path/to/additional.fasta | ||
| transcript_fasta // file: /path/to/transcript.fasta | ||
| gene_bed // file: /path/to/gene.bed | ||
| splicesites // file: /path/to/splicesites.txt | ||
| bbsplit_fasta_list // file: /path/to/bbsplit_fasta_list.txt | ||
| star_index // directory: /path/to/star/index/ | ||
| rsem_index // directory: /path/to/rsem/index/ | ||
| salmon_index // directory: /path/to/salmon/index/ | ||
| kallisto_index // directory: /path/to/kallisto/index/ | ||
| hisat2_index // directory: /path/to/hisat2/index/ | ||
| bbsplit_index // directory: /path/to/rsem/index/ | ||
| gencode // boolean: whether the genome is from GENCODE | ||
| featurecounts_group_type // string: The attribute type used to group feature types in the GTF file when generating the biotype plot with featureCounts | ||
| aligner // string: Specifies the alignment algorithm to use - available options are 'star_salmon', 'star_rsem' and 'hisat2' | ||
| pseudo_aligner // string: Specifies the pseudo aligner to use - available options are 'salmon'. Runs in addition to '--aligner' | ||
| skip_gtf_filter // boolean: Skip filtering of GTF for valid scaffolds and/ or transcript IDs | ||
| skip_bbsplit // boolean: Skip BBSplit for removal of non-reference genome reads | ||
| skip_alignment // boolean: Skip all of the alignment-based processes within the pipeline | ||
| skip_pseudo_alignment // boolean: Skip all of the pseudoalignment-based processes within the pipeline |
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Looking at this, I think this subworkflow is doing waaayyyyy too much.
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| // Determine whether to filter the GTF or not | ||
| def filter_gtf = | ||
| (( | ||
| // Condition 1: Alignment is required and aligner is set | ||
| !skip_alignment && aligner | ||
| ) || | ||
| ( | ||
| // Condition 2: Pseudoalignment is required and pseudoaligner is set | ||
| !skip_pseudo_alignment && pseudo_aligner | ||
| ) || | ||
| ( | ||
| // Condition 3: Transcript FASTA file is not provided | ||
| !transcript_fasta | ||
| )) && | ||
| ( | ||
| // Condition 4: --skip_gtf_filter is not provided | ||
| !skip_gtf_filter | ||
| ) |
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Way too much stuff going on here. We should be able to simplify this by clarifying what filter_gtf means. What are we filtering from the GTF? Why?
| // | ||
| // Print version and exit if required and dump pipeline parameters to JSON file | ||
| // | ||
| UTILS_NEXTFLOW_PIPELINE ( |
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Still not happy with the name UTILS_NEXTFLOW_PIPELINE, NEXTFLOW_PIPELINE_UTILITIES makes more sense but it still doesn't say what the workflow actually does, making it hard to read.
If we didn't know what the subworkflow did, what would we think this was doing?
| def pre_help_text = nfCoreLogo(params.monochrome_logs) | ||
| def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(params.monochrome_logs) | ||
| def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --genome GRCh37 --outdir <OUTDIR>" | ||
| UTILS_NFVALIDATION_PLUGIN ( |
| ======================================================================================== | ||
| */ | ||
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| workflow PIPELINE_INITIALISATION { |
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This name is slightly better, but a function name is a verb so saying what it is doing is more clear for the developer.
| // | ||
| // Custom validation for pipeline parameters | ||
| // | ||
| validateInputParameters() |
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I looked at this and without looking at the code knew exactly what it was doing. A+.
This was referenced Mar 11, 2024
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lib/directory and replace withutils_*subworkflows installed from nf-core/modulesPREPARE_GENOMEsubworkflow to run outside of main rnaseq workflowCUSTOM_DUMPSOFTWAREVERSIONSto use native MultiQC software version reportingtest_cacheprofile as this will be superseded by using test data from S3 whilst porting to nf-test