debug

conf/test.config

@@ -18,5 +18,5 @@ params {
   // Input data
   // 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
-  inputdir = '$baseDir/data'
+  inputdir = './data'
 }

docs/usage.md

@@ -43,18 +43,14 @@ results         # Finished results (configurable, see below)
 
 ## Pipeline arguments
 
-
-
 ### `--contaminant`
 
 Set value define in `conf/genomes.config`. Depend on your pipeline needs.
 
-
 ### `--email myemail@fai.com`
  Set to receive email when pipeline is complete.
 
-
-> Add parameters specific to your pipeline
+> Add here parameters specific to your pipeline
 
 ## Core Nextflow arguments
 

main.nf

@@ -119,8 +119,6 @@ if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) {
 // Stage config files
 ch_multiqc_config = file(params.multiqc_config, checkIfExists: true)
 ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true)
-ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true)
-
 
 
 def summary = [:]
@@ -152,22 +150,6 @@ log.info "-\033[2m--------------------------------------------------\033[0m-"
 log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n")
 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
  */
@@ -191,8 +173,7 @@ process get_software_versions {
     multiqc --version > v_multiqc.txt
     scrape_software_versions.py &> software_versions_mqc.yaml
     """
-    
-
+}
 /*
  * STEP 1 - FastQC
  */
@@ -224,8 +205,6 @@ process qc1 {
     output:
     file("${replicate_id}.qc1") into ch_fastqc_raw_for_assembly
 
-    when: "qc" in step
-
     script:
     """
         echo "mkdir ${replicate_id} ; fastqc --nogroup --quiet -o ${replicate_id} --threads ${task.cpus} ${reads[0]} ${reads[1]}" > ${replicate_id}.qc1
@@ -243,8 +222,6 @@ process assembly {
     output:
     file("${replicate_id}.assembly") into ch_assembly_for_multiqc
 
-    when: "assembly" in step
-
     script:
     """
         echo "ASSEMBLY ${replicate_id} ; " > ${replicate_id}.assembly
@@ -264,7 +241,7 @@ process multiqc {
 
   input:
   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!
   //file ('softwareVersions/*') from softwareVersionsYamlCh.collect().ifEmpty([])
   //file ('workflowSummary/*') from workflowSummaryYamlCh.collect()