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Refactor code and configs #490

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Merged
merged 6 commits into from
Jan 31, 2024
Merged

Refactor code and configs #490

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e6973d7
update schema
ramprasadn Jan 27, 2024
2ec7cf1
refactor
ramprasadn Jan 29, 2024
772c610
update cadd config
ramprasadn Jan 31, 2024
4874b05
Merge branch 'dev' of github.com:nf-core/raredisease into minor-fixes
ramprasadn Jan 31, 2024
217780b
fix case_channel construction
ramprasadn Jan 31, 2024
74458c1
Merge branch 'dev' into minor-fixes
ramprasadn Jan 31, 2024
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9 changes: 8 additions & 1 deletion assets/vep_plugin_files_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,14 @@
"properties": {
"vep_files": {
"type": "string",
"format": "file-path",
"anyOf": [
{
"format": "file-path"
},
{
"format": "directory-path"
}
],
"exists": true,
"errorMessage": "Path to vep plugin files and their indices"
}
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14 changes: 8 additions & 6 deletions conf/modules/align_MT.config
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Expand Up @@ -42,7 +42,7 @@ process {
}

withName: '.*ALIGN_MT:GATK4_MERGEBAMALIGNMENT_MT' {
ext.args = '--CREATE_INDEX true --MAX_GAPS -1 --SORT_ORDER queryname --INCLUDE_SECONDARY_ALIGNMENTS false --PAIRED_RUN false --VALIDATION_STRINGENCY LENIENT'
ext.args = '--TMP_DIR . --CREATE_INDEX true --MAX_GAPS -1 --SORT_ORDER queryname --INCLUDE_SECONDARY_ALIGNMENTS false --PAIRED_RUN false --VALIDATION_STRINGENCY LENIENT'
ext.prefix = { "${meta.id}_merged" }
}

Expand All @@ -52,12 +52,13 @@ process {
"--RGLB lib",
"--RGPL ${params.platform}",
"--RGPU barcode",
"--RGSM ${meta.id}"
"--RGSM ${meta.id}",
"--TMP_DIR ./temp_folder"
].join(' ').trim() }
}

withName: '.*ALIGN_MT:PICARD_MARKDUPLICATES_MT' {
ext.args = '--VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
ext.args = '--TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
ext.prefix = { "${meta.id}_markduplicates" }
}

Expand Down Expand Up @@ -99,7 +100,7 @@ process {
}

withName: '.*ALIGN_MT_SHIFT:GATK4_MERGEBAMALIGNMENT_MT' {
ext.args = '--CREATE_INDEX true --MAX_GAPS -1 --SORT_ORDER queryname --INCLUDE_SECONDARY_ALIGNMENTS false --PAIRED_RUN false --VALIDATION_STRINGENCY LENIENT'
ext.args = '--TMP_DIR . --CREATE_INDEX true --MAX_GAPS -1 --SORT_ORDER queryname --INCLUDE_SECONDARY_ALIGNMENTS false --PAIRED_RUN false --VALIDATION_STRINGENCY LENIENT'
ext.prefix = { "${meta.id}_merged_shifted" }
}

Expand All @@ -109,12 +110,13 @@ process {
"--RGLB lib",
"--RGPL ${params.platform}",
"--RGPU barcode",
"--RGSM ${meta.id}"
"--RGSM ${meta.id}",
"--TMP_DIR ."
].join(' ').trim() }
}

withName: '.*ALIGN_MT_SHIFT:PICARD_MARKDUPLICATES_MT' {
ext.args = '--VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
ext.args = '--TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
ext.prefix = { "${meta.id}_markduplicates_shifted" }
}

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1 change: 1 addition & 0 deletions conf/modules/align_bwa_bwamem2.config
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Expand Up @@ -40,6 +40,7 @@ process {
}

withName: '.*ALIGN:ALIGN_BWA_BWAMEM2:MARKDUPLICATES' {
ext.args = "--TMP_DIR ."
ext.prefix = { "${meta.id}_sorted_md" }
publishDir = [
enabled: !params.save_mapped_as_cram,
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36 changes: 17 additions & 19 deletions conf/modules/annotate_cadd.config
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Expand Up @@ -16,28 +16,26 @@
//

process {
if (params.cadd_resources != null) {
withName: '.*:ANNOTATE_CADD.*' {
ext.when = { ( !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun) }
}
withName: '.*:ANNOTATE_CADD.*' {
ext.when = { ( !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun) }
}

withName: '.*:ANNOTATE_CADD:BCFTOOLS_VIEW' {
ext.args = { "--output-type z --types indels" }
ext.prefix = { "${vcf.simpleName}_indels" }
}
withName: '.*:ANNOTATE_CADD:BCFTOOLS_VIEW' {
ext.args = { "--output-type z --types indels" }
ext.prefix = { "${vcf.simpleName}_indels" }
}

withName: '.*:ANNOTATE_CADD:CADD' {
ext.args = { "-g ${params.genome}" }
ext.prefix = { "${vcf.simpleName}_cadd" }
}
withName: '.*:ANNOTATE_CADD:CADD' {
ext.args = { "-g ${params.genome}" }
ext.prefix = { "${vcf.simpleName}_cadd" }
}

withName: '.*:ANNOTATE_CADD:TABIX_CADD' {
ext.args = { "--force --sequence 1 --begin 2 --end 2" }
}
withName: '.*:ANNOTATE_CADD:TABIX_CADD' {
ext.args = { "--force --sequence 1 --begin 2 --end 2" }
}

withName: '.*:ANNOTATE_CADD:BCFTOOLS_ANNOTATE' {
ext.args = { "--columns Chrom,Pos,Ref,Alt,-,CADD --output-type z" }
ext.prefix = { "${input.simpleName}_ann" }
}
withName: '.*:ANNOTATE_CADD:BCFTOOLS_ANNOTATE' {
ext.args = { "--columns Chrom,Pos,Ref,Alt,-,CADD --output-type z" }
ext.prefix = { "${input.simpleName}_ann" }
}
}
1 change: 1 addition & 0 deletions conf/modules/call_mobile_elements.config
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Expand Up @@ -38,6 +38,7 @@ process {
}

withName: '.*CALL_MOBILE_ELEMENTS:BCFTOOLS_REHEADER_ME' {
ext.args = "--temp-prefix ."
ext.args2 = { '--output-type v' }
ext.prefix = { "${meta.id}_${meta.interval}_retroseq_reheader" }
}
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4 changes: 3 additions & 1 deletion conf/modules/call_repeat_expansions.config
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Expand Up @@ -24,11 +24,12 @@ process {
}

withName: '.*CALL_REPEAT_EXPANSIONS:EXPANSIONHUNTER' {
ext.args = { ("${meta.sex}" == 1) ? '--sex male' : '--sex female' }
ext.args = { ("${meta.sex}" == '1') ? '--sex male' : '--sex female' }
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@jemten jemten Jan 30, 2024

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Was this broken? From the schema it looks like sex needs to be an integer and not a string.

raredisease/assets/schema_input.json

Line 42 in 2be203d

"type": "integer",

I guess that there is a risk that the old ("${meta.sex}" == 1) simply checks for the boolean. Anyway, can you confirm that this sets the gender correctly for male and female?

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@ramprasadn ramprasadn Jan 30, 2024

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Schema does expect the value to be an integer, but in meta everything is of string type.. I retrieved the type of the values in our meta and this is what it looks like..
[id:java.lang.String, sample:java.lang.String, lane:java.lang.String, sex:java.lang.String, phenotype:java.lang.String, paternal:java.lang.String, maternal:java.lang.String, case_id:java.lang.String, num_lanes:java.lang.String, read_group:java.lang.String, single_end:java.lang.Boolean]

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@jemten jemten Jan 31, 2024

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I see, didn't know that :)
In that case we should look into whether this needs changing this as well

raredisease/conf/modules/generate_cytosure_files.config

Line 38 in 2be203d

meta.sex.equals(1) ? '--sex male' : '--sex female',

Worked for my testing previously though
Also it might be worth looking into whether this function needs changing

raredisease/workflows/raredisease.nf

Line 745 in 2be203d

def create_case_channel(List rows) {

ext.prefix = { "${meta.id}_exphunter" }
}

withName: '.*CALL_REPEAT_EXPANSIONS:BCFTOOLS_REHEADER_EXP' {
ext.args = "--temp-prefix ."
ext.prefix = { "${meta.id}_reheader" }
}

Expand Down Expand Up @@ -66,6 +67,7 @@ process {

withName: '.*CALL_REPEAT_EXPANSIONS:COMPRESS_STRANGER' {
ext.prefix = { "${meta.id}_repeat_expansion" }
ext.args = '--output-type z'
publishDir = [
path: { "${params.outdir}/repeat_expansions" },
mode: params.publish_dir_mode,
Expand Down
2 changes: 1 addition & 1 deletion conf/modules/call_snv.config
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Expand Up @@ -20,7 +20,7 @@ process {
}

withName: '.*CALL_SNV:GATK4_SELECTVARIANTS' {
ext.args = "--exclude-intervals ${params.mito_name}"
ext.args = { "--exclude-intervals ${params.mito_name}" }
ext.prefix = { "${meta.id}_nomito" }
publishDir = [
path: { "${params.outdir}/call_snv/genome" },
Expand Down
1 change: 1 addition & 0 deletions conf/modules/call_sv_MT.config
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Expand Up @@ -28,6 +28,7 @@ process {

if (!params.skip_eklipse){
withName: '.*CALL_SV_MT:EKLIPSE' {
ext.args = "-tmp ."
publishDir = [
path: { "${params.outdir}/call_sv/mitochondria" },
mode: params.publish_dir_mode,
Expand Down
12 changes: 6 additions & 6 deletions conf/modules/convert_mt_bam_to_fastq.config
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Expand Up @@ -18,19 +18,19 @@
process {

withName: '.*ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT' {
beforeScript = {"mkdir ./tmp"}
ext.args = [
ext.args = { [
"-L ${params.mito_name}",
"--read-filter MateOnSameContigOrNoMappedMateReadFilter",
"--read-filter MateUnmappedAndUnmappedReadFilter"
].join(" ").trim()
"--read-filter MateUnmappedAndUnmappedReadFilter",
"--tmp-dir ."
].join(" ").trim() }
}

withName: '.*ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_REVERTSAM_MT' {
ext.args = '--OUTPUT_BY_READGROUP false --VALIDATION_STRINGENCY LENIENT --ATTRIBUTE_TO_CLEAR FT --ATTRIBUTE_TO_CLEAR CO --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES false'
ext.args = '--TMP_DIR . --OUTPUT_BY_READGROUP false --VALIDATION_STRINGENCY LENIENT --ATTRIBUTE_TO_CLEAR FT --ATTRIBUTE_TO_CLEAR CO --SORT_ORDER queryname --RESTORE_ORIGINAL_QUALITIES false'
}

withName: '.*ALIGN:CONVERT_MT_BAM_TO_FASTQ:GATK4_SAMTOFASTQ_MT' {
ext.args = '--VALIDATION_STRINGENCY LENIENT'
ext.args = '--VALIDATION_STRINGENCY LENIENT --TMP_DIR .'
}
}
2 changes: 1 addition & 1 deletion conf/modules/postprocess_MT_calls.config
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Expand Up @@ -18,7 +18,7 @@
process {

withName: '.*POSTPROCESS_MT_CALLS:GATK4_MERGEVCFS_LIFT_UNLIFT_MT' {
ext.prefix = { "${meta.id}_merged" }
ext.prefix = { "${meta.id}_merged_liftunlift" }
}

withName: '.*POSTPROCESS_MT_CALLS:GATK4_VARIANTFILTRATION_MT' {
Expand Down
4 changes: 4 additions & 0 deletions conf/modules/qc_bam.config
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Expand Up @@ -25,10 +25,12 @@ process {
}

withName: '.*QC_BAM:PICARD_COLLECTMULTIPLEMETRICS' {
ext.args = "--TMP_DIR ."
ext.prefix = { "${meta.id}_multiplemetrics" }
}

withName: '.*QC_BAM:PICARD_COLLECTHSMETRICS' {
ext.args = "--TMP_DIR ."
ext.when = { !params.target_bed.equals(null) }
ext.prefix = { "${meta.id}_hsmetrics" }
}
Expand Down Expand Up @@ -65,11 +67,13 @@ process {
}

withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS' {
ext.args = "--TMP_DIR ."
ext.when = { params.analysis_type.equals("wgs") && !params.aligner.equals("sentieon") }
ext.prefix = { "${meta.id}_wgsmetrics" }
}

withName: '.*QC_BAM:PICARD_COLLECTWGSMETRICS_Y' {
ext.args = "--TMP_DIR ."
ext.when = { params.analysis_type.equals("wgs") && !params.aligner.equals("sentieon") }
ext.prefix = { "${meta.id}_wgsmetrics_y" }
}
Expand Down
28 changes: 15 additions & 13 deletions workflows/raredisease.nf
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Expand Up @@ -312,17 +312,19 @@ workflow RAREDISEASE {
}

// Read and store paths in the vep_plugin_files file
ch_vep_extra_files_unsplit.splitCsv ( header:true )
.map { row ->
f = file(row.vep_files[0])
if(f.isFile() || f.isDirectory()){
return [f]
} else {
error("\nVep database file ${f} does not exist.")
if (params.vep_plugin_files) {
ch_vep_extra_files_unsplit.splitCsv ( header:true )
.map { row ->
f = file(row.vep_files[0])
if(f.isFile() || f.isDirectory()){
return [f]
} else {
error("\nVep database file ${f} does not exist.")
}
}
}
.collect()
.set {ch_vep_extra_files}
.collect()
.set {ch_vep_extra_files}
}

// Input QC
if (!params.skip_fastqc) {
Expand Down Expand Up @@ -760,13 +762,13 @@ def create_case_channel(List rows) {
if (item.phenotype == 2) {
probands.add(item.sample)
}
if ( (item.paternal!=0) && (item.paternal!="") && (item.maternal!=0) && (item.maternal!="") ) {
if ( (item.paternal!="0") && (item.paternal!="") && (item.maternal!="0") && (item.maternal!="") ) {
upd_children.add(item.sample)
}
if ( (item.paternal!=0) && (item.paternal!="") ) {
if ( (item.paternal!="0") && (item.paternal!="") ) {
father = item.paternal
}
if ( (item.maternal!=0) && (item.maternal!="") ) {
if ( (item.maternal!="0") && (item.maternal!="") ) {
mother = item.maternal
}
}
Expand Down