Closed
Conversation
added 8 commits
December 13, 2021 16:25
linting update publishDir linting
FriederikeHanssen
requested changes
Dec 13, 2021
Contributor
FriederikeHanssen
left a comment
FriederikeHanssen
left a comment
There was a problem hiding this comment.
hey @nickhsmith thanks a lot for fixing the publish copy issue 😊 anything that is not right in nf-core/modules should be fixed in that repository, so we can properly pull from there. Since you have also adressed some of the null/false things in the nextflow.config here, maybe we can wait for conclusion on the discussion and Maxime to merge his PR. We could certainly add the things about Haplotypecaller here, and once Gavin is ready just overwrite it.
| ext.args = { meta.status == 1 ? '-K 100000000 -M -B 3' : '-K 100000000 -M' } | ||
| publishDir = [ enabled: false ] | ||
| ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat(reads.get(0).name.findAll(/part_([0-9]+)?/).last().concat('.')) : "${meta.id}" } | ||
| publishDir = [ |
Contributor
There was a problem hiding this comment.
if it is not enabled, i don't think this needs to be here
Contributor
Author
There was a problem hiding this comment.
I like having the same format, and if someone decides tomorrow to output/publish this module. All they need to do is to change enabled But it's definitely not used now
|
|
||
| withName: 'SAMTOOLS_MERGE' { | ||
| publishDir = [ enabled: false ] | ||
| publishDir = [ |
| withName: 'SEQKIT_SPLIT2' { | ||
| ext.args = { "--by-size ${params.split_fastq}" } | ||
| publishDir = [ enabled: false ] | ||
| publishDir = [ |
| publishDir = [ | ||
| path: { "${params.outdir}/preprocessing/${meta.id}/markduplicates" }, | ||
| enabled: false | ||
| enabled: false, |
Contributor
There was a problem hiding this comment.
see above, and the path could actually also be removed
| } | ||
|
|
||
| if (params.step == 'preparerecalibration') { | ||
| if (params.step == 'prepare_recalibration') { |
Contributor
There was a problem hiding this comment.
Suggested change
| if (params.step == 'prepare_recalibration') { | |
| if (params.step == 'preparerecalibration') { |
| case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break | ||
| case 'recalibrate': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates.csv", checkIfExists: true); break | ||
| case 'variantcalling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break | ||
| case 'variant_calling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break |
Contributor
There was a problem hiding this comment.
Suggested change
| case 'variant_calling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break | |
| case 'variantcalling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break |
| switch (params.step) { | ||
| case 'mapping': exit 1, "Can't start with step $params.step without samplesheet" | ||
| case 'preparerecalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break | ||
| case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break |
Contributor
There was a problem hiding this comment.
Suggested change
| case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break | |
| case 'preparerecalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break |
|
|
||
| ch_known_indels_tbi = Channel.empty() | ||
| if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step)) { | ||
| if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'prepare_recalibration' in step)) { |
Contributor
There was a problem hiding this comment.
Suggested change
| if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'prepare_recalibration' in step)) { | |
| if (!(params.known_indels_tbi) && params.known_indels && ('mapping' in step || 'preparerecalibration' in step)) { |
subworkflows/local/prepare_genome.nf
Outdated
|
|
||
| ch_dbsnp_tbi = Channel.empty() | ||
| if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { | ||
| if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'prepare_recalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { |
Contributor
There was a problem hiding this comment.
Suggested change
| if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'prepare_recalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { | |
| if (!(params.dbsnp_tbi) && params.dbsnp && ('mapping' in step || 'preparerecalibration' in step || 'controlfreec' in tools || 'haplotypecaller' in tools|| 'mutect2' in tools || 'tnscope' in tools)) { |
Contributor
|
Before we can merge for sure, need to get the CI tests back to pass as well as the linting for sure 🙈 |
| @@ -1,6 +1,5 @@ | |||
| params { | |||
| outdir = "output/" | |||
| publish_dir_mode = "copy" | |||
Contributor
There was a problem hiding this comment.
I think this might need to stay in for the CI tests to pass
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Member
|
You can check #468 for some updates, but we're probably going to get another PR whenever the tools release is happening (which I guess should be soon now) |
|
maxulysse
reviewed
Feb 14, 2022
Comment on lines
-74
to
-79
|
|
||
| // Check input has been provided | ||
| if (!params.input) { | ||
| log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" | ||
| System.exit(1) | ||
| } |
Contributor
Author
There was a problem hiding this comment.
we need to have some work around for utilizing the automatic restart. This check totally negates the checks at workflows/sarek.nf lines 46 - 56
Contributor
There was a problem hiding this comment.
hm ok I would say we need to fix sarek not the template then, what do you think?
Contributor
Author
There was a problem hiding this comment.
I think it's quite a useful feature to be able to restart the analysis. There is already a warning, and if the step isn't there it throws an error. You need to designate a step, which essentially is a shortcut for editing the config file. just set step = variant_calling instead of input = 'Path/To/Dir/preprocessing/csv/recalibrated.csv'
Contributor
There was a problem hiding this comment.
right, I definitly think we should keep it, just make it work properly without messing with the template :)
Contributor
There was a problem hiding this comment.
or otherwise we should raise the issue in tools and see i the template needs changing
maxulysse
reviewed
Feb 14, 2022
Comment on lines
+380
to
+383
| <<<<<<< HEAD | ||
| ======= | ||
|
|
||
| >>>>>>> f1bcc423664ba9bcec1cd227225555971ef87a63 |
Member
There was a problem hiding this comment.
Suggested change
| <<<<<<< HEAD | |
| ======= | |
| >>>>>>> f1bcc423664ba9bcec1cd227225555971ef87a63 |
Member
|
Still some comments not addressed, but looking better and better, I like the update on concat_vcf |
Contributor
Author
|
This whole PR is still not right or up to date. But There is good conversation here. |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).This PR seeks to fix 2 problems.
path,mode,pattern, andenabledkeywords. This should now address [BUG] modules.config: publishDirmode: 'copy' #471 and match the module stle