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Fix large comment block headers so they don't cause phantom merge con… #6755

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merged 3 commits into from
Oct 9, 2024
Merged

Fix large comment block headers so they don't cause phantom merge con… #6755

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cc41a97
Fix large comment block headers so they don't cause phantom merge con…
jfy133 Oct 8, 2024
1b0bab5
Apply suggestions from code review
mirpedrol Oct 9, 2024
e43f1c5
fix color code
mirpedrol Oct 9, 2024
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10 changes: 5 additions & 5 deletions modules/nf-core/ensemblvep/filtervep/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running tests
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
params {
vep_cache_version = "112"
vep_genome = "WBcel235"
vep_species = "caenorhabditis_elegans"
vep_cache_version = "112"
vep_genome = "WBcel235"
vep_species = "caenorhabditis_elegans"
}
8 changes: 4 additions & 4 deletions modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running tests
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

process {
Expand All @@ -13,12 +13,12 @@ process {
}

withName: ENSEMBLVEP_VEP {
ext.args = '--tab'
ext.args = '--tab'
ext.prefix = { "${meta.id}_vep" }
}

withName: ENSEMBLVEP_FILTERVEP {
ext.args = '--filter "Feature_type is Transcript"'
ext.args = '--filter "Feature_type is Transcript"'
ext.suffix = "tab"
}
}
6 changes: 3 additions & 3 deletions modules/nf-core/ensemblvep/filtervep/tests/vcf.config
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running tests
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

process {
Expand All @@ -13,7 +13,7 @@ process {
}

withName: ENSEMBLVEP_VEP {
ext.args = '--vcf'
ext.args = '--vcf'
ext.prefix = { "${meta.id}_vep" }
}

Expand Down
46 changes: 22 additions & 24 deletions subworkflows/nf-core/utils_nextflow_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,12 @@
//

/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SUBWORKFLOW DEFINITION
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

workflow UTILS_NEXTFLOW_PIPELINE {

take:
print_version // boolean: print version
dump_parameters // boolean: dump parameters
Expand All @@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
// Print workflow version and exit on --version
//
if (print_version) {
log.info "${workflow.manifest.name} ${getWorkflowVersion()}"
log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
System.exit(0)
}

Expand All @@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE {
}

/*
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
FUNCTIONS
========================================================================================
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

//
Expand All @@ -72,11 +71,11 @@ def getWorkflowVersion() {
// Dump pipeline parameters to a JSON file
//
def dumpParametersToJSON(outdir) {
def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
def filename = "params_${timestamp}.json"
def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
def jsonStr = groovy.json.JsonOutput.toJson(params)
temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr)
def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
def filename = "params_${timestamp}.json"
def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
def jsonStr = groovy.json.JsonOutput.toJson(params)
temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr)

nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
temp_pf.delete()
Expand All @@ -91,9 +90,14 @@ def checkCondaChannels() {
try {
def config = parser.load("conda config --show channels".execute().text)
channels = config.channels
} catch(NullPointerException | IOException e) {
log.warn "Could not verify conda channel configuration."
return
}
catch (NullPointerException e) {
log.warn("Could not verify conda channel configuration.")
return null
}
catch (IOException e) {
log.warn("Could not verify conda channel configuration.")
return null
}

// Check that all channels are present
Expand All @@ -106,19 +110,13 @@ def checkCondaChannels() {

required_channels_in_order.eachWithIndex { channel, index ->
if (index < required_channels_in_order.size() - 1) {
channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1]))
}
}

if (channels_missing | channel_priority_violation) {
log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
" There is a problem with your Conda configuration!\n\n" +
" You will need to set-up the conda-forge and bioconda channels correctly.\n" +
" Please refer to https://bioconda.github.io/\n" +
" The observed channel order is \n" +
" ${channels}\n" +
" but the following channel order is required:\n" +
" ${required_channels_in_order}\n" +
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
log.warn(
"~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
)
Comment on lines -114 to +120
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I tried to preserve the formatting here but found it to be tricky, probably a multi-line string would be better anyway:

    log.warn """\
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
          There is a problem with your Conda configuration!

          You will need to set-up the conda-forge and bioconda channels correctly.
          Please refer to https://bioconda.github.io/
          The observed channel order is 
          ${channels}
          but the following channel order is required:
          ${required_channels_in_order}
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        """.stripIndent(true)

}
}
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