Skip to content

Automatic restart #560

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
FriederikeHanssen wants to merge 3 commits into from
Closed

Automatic restart #560

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
aa12173
remove input from required options
FriederikeHanssen May 24, 2022
a35365c
allow optional input param again
FriederikeHanssen May 24, 2022
f235ea5
remove unuse no_strlka_bp
FriederikeHanssen May 24, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
27 changes: 25 additions & 2 deletions lib/WorkflowMain.groovy
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -74,8 +74,31 @@ class WorkflowMain {

// 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)
log.warn "No samplesheet specified, attempting to restart from csv files present in ${params.outdir}"

switch (params.step) {
case 'mapping': log.warn "Can't start with step $params.step without samplesheet"
System.exit(1);
break
//case 'markduplicates': log.warn "Using file ${params.outdir}/preprocessing/csv/markduplicates_no_table.csv"
// params.input = "${params.outdir}/preprocessing/csv/markduplicates_no_table.csv";
// break
case 'prepare_recalibration': log.warn "Using file ${params.outdir}/preprocessing/csv/markduplicates_no_table.csv"
params.input = "${params.outdir}/preprocessing/csv/markduplicates_no_table.csv";
break
case 'recalibrate': log.warn "Using file ${params.outdir}/preprocessing/csv/markduplicates.csv"
params.input = "${params.outdir}/preprocessing/csv/markduplicates.csv";
break
case 'variant_calling': log.warn "Using file ${params.outdir}/preprocessing/csv/recalibrated.csv"
params.input = "${params.outdir}/preprocessing/csv/recalibrated.csv";
break
// // case 'controlfreec': csv_file = file("${params.outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break
// case 'annotate': csv_file = file("${params.outdir}/variant_calling/csv/recalibrated.csv", checkIfExists: true); break
default: log.warn "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
exit 1, "Unknown step $params.step"

//log.warn "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
//System.exit(1)
}
}

Expand Down
1 change: 0 additions & 1 deletion nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,6 @@ params {
cf_window = null // by default we are not using this in Control-FREEC

generate_gvcf = false // g.vcf are not produced by HaplotypeCaller by default
no_strelka_bp = false // Strelka will use Manta candidateSmallIndels if available
pon = null // No default PON (Panel of Normals) file for GATK Mutect2 / Sentieon TNscope
pon_tbi = null // No default PON index for GATK Mutect2 / Sentieon TNscope
ignore_soft_clipped_bases = false // no --dont-use-soft-clipped-bases for GATK Mutect2
Expand Down
8 changes: 1 addition & 7 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["step", "input", "outdir"],
"required": ["step", "outdir"],
"properties": {
"step": {
"type": "string",
Expand Down Expand Up @@ -294,12 +294,6 @@
"fa_icon": "fas fa-copy",
"description": "Generate g.vcf output from GATK HaplotypeCaller."
},
"no_strelka_bp": {
"type": "boolean",
"fa_icon": "fas fa-ban",
"description": "Will not use Manta candidateSmallIndels for Strelka.",
"help_text": "Not recommended by Best Practices."
},
"pon": {
"type": "string",
"fa_icon": "fas fa-file",
Expand Down
32 changes: 16 additions & 16 deletions workflows/sarek.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -46,22 +46,22 @@ def checkPathParamList = [
for (param in checkPathParamList) if (param) file(param, checkIfExists: true)

// Check mandatory parameters
if (params.input) csv_file = file(params.input)
else {
log.warn "No samplesheet specified, attempting to restart from csv files present in ${params.outdir}"
switch (params.step) {
case 'mapping': exit 1, "Can't start with step $params.step without samplesheet"
//case 'markduplicates': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break
case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break
case 'recalibrate': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates.csv", checkIfExists: true); break
case 'variant_calling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break
// case 'controlfreec': csv_file = file("${params.outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break
case 'annotate': csv_file = file("${params.outdir}/variant_calling/csv/recalibrated.csv", checkIfExists: true); break
default: exit 1, "Unknown step $params.step"
}
}

ch_input_sample = extract_csv(csv_file)
// if (params.input) csv_file = file(params.input, checkIfExists: true)
// else {
// log.warn "No samplesheet specified, attempting to restart from csv files present in ${params.outdir}"
// // switch (params.step) {
// // case 'mapping': exit 1, "Can't start with step $params.step without samplesheet"
// // //case 'markduplicates': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break
// // case 'prepare_recalibration': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates_no_table.csv", checkIfExists: true); break
// // case 'recalibrate': csv_file = file("${params.outdir}/preprocessing/csv/markduplicates.csv", checkIfExists: true); break
// // case 'variant_calling': csv_file = file("${params.outdir}/preprocessing/csv/recalibrated.csv", checkIfExists: true); break
// // // case 'controlfreec': csv_file = file("${params.outdir}/variant_calling/csv/control-freec_mpileup.csv", checkIfExists: true); break
// // case 'annotate': csv_file = file("${params.outdir}/variant_calling/csv/recalibrated.csv", checkIfExists: true); break
// // default: exit 1, "Unknown step $params.step"
// // }
// }

ch_input_sample = extract_csv(file(params.input, checkIfExists: true))

if (params.wes) {
if (params.intervals && !params.intervals.endsWith("bed")) exit 1, "Target file must be in BED format"
Expand Down
⚡