General cleanup #447
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General cleanup #447
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…nto issue_400 Please enter a commit message to explain why this merge is necessary,
atrigila
reviewed
Sep 30, 2024
subworkflows/local/mirdeep2.nf
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This file was removed in latest dev
workflows/smrnaseq.nf
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| ch_three_prime_adapter = Channel.value(params.three_prime_adapter) | ||
| ch_phred_offset = Channel.value(params.phred_offset) |
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These should be in prepare_genome or pipeline initialisation
| bowtie_index = ch_bowtie_index // channel: [genome.1.ebwt, genome.2.ebwt, genome.3.ebwt, genome.4.ebwt, genome.rev.1.ebwt, genome.rev.2.ebwt] | ||
| bowtie_index = ch_bowtie_index // channel: [ val(meta), path(index) ] |
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If the user inputs the index from a .tar.gz we need to make sure it has this structure. I think currently it has the previous structure (genome.ebwt, etc).
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This was updated in a previous PR, it now has a meta , but I had forgotten to update the channel comment.
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Cool. We can simply have the channel to be [id:"bowtie_index", [workspace/etc/bowtie_index]]. It does not have to have the path to the ebwt files as the modules can handle the whole directory (and mirdeep cannot handle it without the directory).
subworkflows/local/mirna_quant.nf
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Perhaps the module and file name table_merge and datatable_merge can have the same name for consistency. Also have a main.nf file.
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Same applies to edger_qc. Should be main.nf.
modules.json
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pigz_uncompress is no longer used and can be removed
modules.json
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untarfiles shall be replaced by untar
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This is not straightforward, lets do it on a separate PR: https://github.com/orgs/nf-core/projects/74/views/7?pane=issue&itemId=81583371
workflows/smrnaseq.nf
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| @@ -53,9 +53,9 @@ workflow NFCORE_SMRNASEQ { | |||
| ch_reference_hairpin // channel: [ val(meta), path(fasta) ] | |||
| ch_mirna_gtf // channel: [ path(GTF) ] | |||
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Would it be useful for ch_mirna_gtf to have a meta as well?
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We don't need it, but will add it for consistency
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Are we addressing the whole scope of #400 or some sub-tasks here (in this PR)?
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Ah, I see, yes we adressing all of the items in the issue, we could also add, I will also add, reviewing parameters modules and subworkflows to check there are no unused items. |
atrigila
reviewed
Sep 30, 2024
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I've also run nf-core lint to check TODOs left in the pipeline and found a few issues:
╭───────────────────────╮
│ LINT RESULTS SUMMARY │
├───────────────────────┤
│ [✔] 460 Tests Passed │
│ [?] 1 Test Ignored │
│ [!] 26 Test Warnings │
│ [✗] 1 Test Failed │
╰───────────────────────╯
subworkflows/local/genome_quant.nf
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| @@ -7,7 +7,7 @@ include { BOWTIE_ALIGN as BOWTIE_MAP_GENOME } from '../../modules/nf-core/bowtie | |||
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| workflow GENOME_QUANT { | |||
| take: | |||
| ch_bowtie_index // channel: [genome.1.ebwt, genome.2.ebwt, genome.3.ebwt, genome.4.ebwt, genome.rev.1.ebwt, genome.rev.2.ebwt] | |||
| ch_bowtie_index // channel: [ val(meta), [ path(genome.1.ebwt), path(genome.2.ebwt), path(genome.3.ebwt), path(genome.4.ebwt), path(genome.rev.1.ebwt), path(genome.rev.2.ebwt) ] ] | |||
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Sorry if I wasn't clear in my previous comment, but for this to work in mirdeep2 ch_bowtie_index should be of structure:
channel: [ val(meta), [ path(one_directory)] and not
channel: [ val(meta), [ path(genome.1.ebwt), path(genome.2.ebwt), path(genome.3.ebwt), path(genome.4.ebwt), path(genome.rev.1.ebwt), path(genome.rev.2.ebwt) ] ].
Please write me if we need to review this together.
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This is something that is a bit more tricky to update, I created a new ticket to address it: #451
| @@ -55,7 +55,7 @@ workflow PREPARE_GENOME { | |||
| ch_bowtie_index = UNTAR_BOWTIE_INDEX.out.files | |||
| ch_versions = ch_versions.mix(UNTAR_BOWTIE_INDEX.out.versions) | |||
| } else { | |||
| ch_bowtie_index = Channel.fromPath("${val_bowtie_index}**ebwt", checkIfExists: true).map{it -> [ [id:it.baseName], it ] }.collect() | |||
| ch_bowtie_index = Channel.fromPath("${val_bowtie_index}**ebwt", checkIfExists: true).map{it -> [ [id:'bowtie_index'], it ] }.collect() | |||
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Mirdeep2 is a bit tricky in how the index should be named:
So if the path to the index ch_bowtie_index is something like:
/work/bowtie_index
and the files inside that directory are:
/work/bowtie_index/genome.1.ebwt
/work/bowtie_index/genome.2.ebwt
/work/bowtie_index/genome.3.ebwt
Then the meta should be: genome.
This renaming is done automatically when indexing the fasta in the else statement:
// Index FASTA with nf-core Bowtie1
INDEX_GENOME ( CLEAN_FASTA.out.output )
ch_versions = ch_versions.mix(INDEX_GENOME.out.versions)
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Also to be addressed in #451
| } | ||
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| emit: | ||
| fasta = ch_fasta // channel: [ val(meta), path(fasta) ] | ||
| has_fasta = bool_has_fasta // boolean | ||
| bowtie_index = ch_bowtie_index // channel: [genome.1.ebwt, genome.2.ebwt, genome.3.ebwt, genome.4.ebwt, genome.rev.1.ebwt, genome.rev.2.ebwt] | ||
| bowtie_index = ch_bowtie_index // channel: [ val(meta), [ path(genome.1.ebwt), path(genome.2.ebwt), path(genome.3.ebwt), path(genome.4.ebwt), path(genome.rev.1.ebwt), path(genome.rev.2.ebwt) ] ] |
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Same comment, due to how mirdeep2 is structured this should have the structure: channel: [ val(meta), [ path(directory_index)] ]
| ch_bowtie_index // channel: [ val(meta), index ] | ||
| ch_bowtie_index // channel: [ val(meta), [ path(genome.1.ebwt), path(genome.2.ebwt), path(genome.3.ebwt), path(genome.4.ebwt), path(genome.rev.1.ebwt), path(genome.rev.2.ebwt) ] ] |
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This should not be changed in a nf-core subworkflow as it will break linting.
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You are right, lets take care of it in #451
apeltzer
approved these changes
Sep 30, 2024
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PR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).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).