From bf3928eb2ddeb120c8b4db18b405bba3f4bb2c7c Mon Sep 17 00:00:00 2001
From: jessicaw9910 <jessbwhite@gmail.com>
Date: Fri, 19 Jul 2024 13:19:12 -0400
Subject: [PATCH] turned sub-directories into params and removed unnecessary
 sub-dirs for MultiQC reports

---
 nextflow/main.nf | 38 ++++++++++++++++++++++++--------------
 1 file changed, 24 insertions(+), 14 deletions(-)

diff --git a/nextflow/main.nf b/nextflow/main.nf
index 0ca9067..d8e61ea 100644
--- a/nextflow/main.nf
+++ b/nextflow/main.nf
@@ -12,15 +12,25 @@
 params.max_memory = "64.GB"
 params.max_cpus = 12
 
-params.fastq = "${params.inputDir}${params.fastqFile}"
+// sub-directories - only FastQC needs additional sub-dir
+params.dirFastQC = "fastqc"
+params.dirFastp = "fastqp"
+params.dirMultiQC = "multiqc"
+params.dirAlignment = "alignment"
 
-params.fastp = "${params.outDir}/fastp/*_{1,2}.fastp*"
-params.fastp_json = "${params.outDir}/fastp/*fastp.json"
+// fastq
+params.fastq = "${params.inputDir}/${params.fastqFile}"
 
-params.fastqc_fastq = "${params.outDir}/fastqc/fastq/*/*"
-params.fastqc_fastp = "${params.outDir}/fastqc/fastp/*/*"
+// fastp
+params.fastp = "${params.outDir}/${params.dirFastp}/*_{1,2}.fastp*"
+params.fastp_json = "${params.outDir}/${params.dirFastp}/*fastp.json"
 
-params.bam = "${params.outDir}/alignment/*.Aligned.sortedByCoord.out.bam"
+// fastqc
+params.fastqc_fastq = "${params.outDir}/${params.dirFastQC}/fastq/*/*"
+params.fastqc_fastp = "${params.outDir}/${params.dirFastQC}/fastp/*/*"
+
+// bam
+params.bam = "${params.outDir}/${params.dirAlignment}/*.Aligned.sortedByCoord.out.bam"
 
 log.info """\
         STAR RNA-Seq NextFlow Pipeline (Reference-Based)
@@ -42,20 +52,20 @@ log.info """\
 */
 
 // pre-trimming QC fastqc and multiqc
-include { RUN_FASTQC  as RUN_FASTQC_FASTQ  } from './modules/fastqc/main.nf'   addParams(OUTPUT: "${params.outDir}/fastqc/fastq")
-include { RUN_MULTIQC as RUN_MULTIQC_FASTQ } from './modules/multiqc/main.nf'  addParams(OUTPUT: "${params.outDir}/multiqc/fastq")
+include { RUN_FASTQC  as RUN_FASTQC_FASTQ  } from './modules/fastqc/main.nf'   addParams(OUTPUT: "${params.outDir}/${params.dirFastQC}/fastq")
+include { RUN_MULTIQC as RUN_MULTIQC_FASTQ } from './modules/multiqc/main.nf'  addParams(OUTPUT: "${params.outDir}/${params.dirMultiQC}")
 
 // trimming with fastp and pre-alignment QC fastqc and multiqc
-include { RUN_FASTP                        } from './modules/fastp/main.nf'    addParams(OUTPUT: "${params.outDir}/fastp")
-include { RUN_FASTQC  as RUN_FASTQC_FASTP  } from './modules/fastqc/main.nf'   addParams(OUTPUT: "${params.outDir}/fastqc/fastp")
-include { RUN_MULTIQC as RUN_MULTIQC_FASTP } from './modules/multiqc/main.nf'  addParams(OUTPUT: "${params.outDir}/multiqc/fastp")
+include { RUN_FASTP                        } from './modules/fastp/main.nf'    addParams(OUTPUT: "${params.outDir}/${params.dirFastp}")
+include { RUN_FASTQC  as RUN_FASTQC_FASTP  } from './modules/fastqc/main.nf'   addParams(OUTPUT: "${params.outDir}/${params.dirFastQC}/fastp")
+include { RUN_MULTIQC as RUN_MULTIQC_FASTP } from './modules/multiqc/main.nf'  addParams(OUTPUT: "${params.outDir}/${params.dirMultiQC}")
 
 // align fastq files using STAR and index
-include { STAR_ALIGN                       } from './modules/star/main.nf'     addParams(OUTPUT: "${params.outDir}/alignment")
-include { SAMTOOLS_INDEX                   } from './modules/samtools/main.nf' addParams(OUTPUT: "${params.outDir}/alignment")
+include { STAR_ALIGN                       } from './modules/star/main.nf'     addParams(OUTPUT: "${params.outDir}/${params.dirAlignment}")
+include { SAMTOOLS_INDEX                   } from './modules/samtools/main.nf' addParams(OUTPUT: "${params.outDir}/${params.dirAlignment}")
 
 // post-alignment multiqc
-include { RUN_MULTIQC as RUN_MULTIQC_STAR  } from './modules/multiqc/main.nf'  addParams(OUTPUT: "${params.outDir}/multiqc/bam")
+include { RUN_MULTIQC as RUN_MULTIQC_STAR  } from './modules/multiqc/main.nf'  addParams(OUTPUT: "${params.outDir}/${params.dirMultiQC}")
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~