Merge pull request #10 from CDCgov/dev

hseabolt · web-flow · commit 7030cd861214 · 2023-08-15T16:11:01.000-04:00
Dev
diff --git a/workflows/aquascope.nf b/workflows/aquascope.nf
@@ -108,7 +108,6 @@ workflow AQUASCOPE {
     FASTQC_RAW_LONG (
         ch_long_reads
     )
-    ch_versions = ch_versions.mix(FASTQC_RAW_LONG.out.versions.first())
 
     // 
     // MODULE: Run FastP for short reads
@@ -128,7 +127,6 @@ workflow AQUASCOPE {
         ch_long_reads, [], false, false
     )
     ch_trimmed_reads_long = ch_trimmed_reads_long.mix(FASTP_LONG.out.reads)
-    ch_versions = ch_versions.mix(FASTP_LONG.out.versions.first())
 
     // Combine trimmed reads from short and long reads
     ch_trimmed_reads = ch_trimmed_reads_short.mix(ch_trimmed_reads_long)
@@ -141,7 +139,6 @@ workflow AQUASCOPE {
     FASTQC_TRIMMED (
         ch_trimmed_reads
     )
-    ch_versions = ch_versions.mix(FASTQC_TRIMMED.out.versions.first())
     
     // 
     // MODULE: Align reads against reference genome

Original file line number	Diff line number	Diff line change
`@@ -108,7 +108,6 @@ workflow AQUASCOPE {`
`108`	`108`	`FASTQC_RAW_LONG (`
`109`	`109`	`ch_long_reads`
`110`	`110`	`)`
`111`		`- ch_versions = ch_versions.mix(FASTQC_RAW_LONG.out.versions.first())`
`112`	`111`
`113`	`112`	`//`
`114`	`113`	`// MODULE: Run FastP for short reads`
`@@ -128,7 +127,6 @@ workflow AQUASCOPE {`
`128`	`127`	`ch_long_reads, [], false, false`
`129`	`128`	`)`
`130`	`129`	`ch_trimmed_reads_long = ch_trimmed_reads_long.mix(FASTP_LONG.out.reads)`
`131`		`- ch_versions = ch_versions.mix(FASTP_LONG.out.versions.first())`
`132`	`130`
`133`	`131`	`// Combine trimmed reads from short and long reads`
`134`	`132`	`ch_trimmed_reads = ch_trimmed_reads_short.mix(ch_trimmed_reads_long)`
`@@ -141,7 +139,6 @@ workflow AQUASCOPE {`
`141`	`139`	`FASTQC_TRIMMED (`
`142`	`140`	`ch_trimmed_reads`
`143`	`141`	`)`
`144`		`- ch_versions = ch_versions.mix(FASTQC_TRIMMED.out.versions.first())`
`145`	`142`
`146`	`143`	`//`
`147`	`144`	`// MODULE: Align reads against reference genome`