Commit 5f64b280 authored by Celine Noirot's avatar Celine Noirot
Browse files

debug

parent 61422432
...@@ -18,5 +18,5 @@ params { ...@@ -18,5 +18,5 @@ params {
// Input data // Input data
// TODO nf-core: Specify the paths to your test data on nf-core/test-datasets // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
// TODO nf-core: Give any required params for the test so that command line flags are not needed // TODO nf-core: Give any required params for the test so that command line flags are not needed
inputdir = '$baseDir/data' inputdir = './data'
} }
...@@ -43,18 +43,14 @@ results # Finished results (configurable, see below) ...@@ -43,18 +43,14 @@ results # Finished results (configurable, see below)
## Pipeline arguments ## Pipeline arguments
### `--contaminant` ### `--contaminant`
Set value define in `conf/genomes.config`. Depend on your pipeline needs. Set value define in `conf/genomes.config`. Depend on your pipeline needs.
### `--email myemail@fai.com` ### `--email myemail@fai.com`
Set to receive email when pipeline is complete. Set to receive email when pipeline is complete.
> Add here parameters specific to your pipeline
> Add parameters specific to your pipeline
## Core Nextflow arguments ## Core Nextflow arguments
......
...@@ -119,8 +119,6 @@ if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) { ...@@ -119,8 +119,6 @@ if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
// Stage config files // Stage config files
ch_multiqc_config = file(params.multiqc_config, checkIfExists: true) ch_multiqc_config = file(params.multiqc_config, checkIfExists: true)
ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true) ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
def summary = [:] def summary = [:]
...@@ -152,22 +150,6 @@ log.info "-\033[2m--------------------------------------------------\033[0m-" ...@@ -152,22 +150,6 @@ log.info "-\033[2m--------------------------------------------------\033[0m-"
log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n") log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
log.info "-\033[2m--------------------------------------------------\033[0m-" log.info "-\033[2m--------------------------------------------------\033[0m-"
/* In case of modular pipeline*/
params.step = "qc"
availableStepList =
[
'qc',
'assembly',
'filtering',
'binning'
]
/*Check if step exist in stepList*/
step = params.step.split(",")
for (String a_step: step) {
assert (a_step in availableStepList)
}
/* /*
* Parse software version numbers * Parse software version numbers
*/ */
...@@ -191,8 +173,7 @@ process get_software_versions { ...@@ -191,8 +173,7 @@ process get_software_versions {
multiqc --version > v_multiqc.txt multiqc --version > v_multiqc.txt
scrape_software_versions.py &> software_versions_mqc.yaml scrape_software_versions.py &> software_versions_mqc.yaml
""" """
}
/* /*
* STEP 1 - FastQC * STEP 1 - FastQC
*/ */
...@@ -224,8 +205,6 @@ process qc1 { ...@@ -224,8 +205,6 @@ process qc1 {
output: output:
file("${replicate_id}.qc1") into ch_fastqc_raw_for_assembly file("${replicate_id}.qc1") into ch_fastqc_raw_for_assembly
when: "qc" in step
script: script:
""" """
echo "mkdir ${replicate_id} ; fastqc --nogroup --quiet -o ${replicate_id} --threads ${task.cpus} ${reads[0]} ${reads[1]}" > ${replicate_id}.qc1 echo "mkdir ${replicate_id} ; fastqc --nogroup --quiet -o ${replicate_id} --threads ${task.cpus} ${reads[0]} ${reads[1]}" > ${replicate_id}.qc1
...@@ -243,8 +222,6 @@ process assembly { ...@@ -243,8 +222,6 @@ process assembly {
output: output:
file("${replicate_id}.assembly") into ch_assembly_for_multiqc file("${replicate_id}.assembly") into ch_assembly_for_multiqc
when: "assembly" in step
script: script:
""" """
echo "ASSEMBLY ${replicate_id} ; " > ${replicate_id}.assembly echo "ASSEMBLY ${replicate_id} ; " > ${replicate_id}.assembly
...@@ -264,7 +241,7 @@ process multiqc { ...@@ -264,7 +241,7 @@ process multiqc {
input: input:
file (multiqc_config) from ch_multiqc_config file (multiqc_config) from ch_multiqc_config
file ('fastqc/*') from fastqc_results_for_multiqc.collect().ifEmpty([]) file ('fastqc/*') from ch_fastqc_results_for_multiqc.collect().ifEmpty([])
// TODO get-nf: Add in log files from your new processes for MultiQC to find! // TODO get-nf: Add in log files from your new processes for MultiQC to find!
//file ('softwareVersions/*') from softwareVersionsYamlCh.collect().ifEmpty([]) //file ('softwareVersions/*') from softwareVersionsYamlCh.collect().ifEmpty([])
//file ('workflowSummary/*') from workflowSummaryYamlCh.collect() //file ('workflowSummary/*') from workflowSummaryYamlCh.collect()
......
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