adding "-trim" to the nextseq cmd in conf. see #429

cmatKhan · cmatKhan · commit 750d8060950c · 2024-10-21T12:51:02.000-05:00
diff --git a/conf/modules.config b/conf/modules.config
@@ -135,7 +135,7 @@ if (!params.skip_trimming) {
             ext.args   = {
                 [
                     '--fastqc',
-                    params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : '',
+                    params.trim_nextseq > 0 ? "--nextseq-trim ${params.trim_nextseq}" : '',
                     params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : '',
                     params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : '',
                     params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : '',

Original file line number	Diff line number	Diff line change
`@@ -135,7 +135,7 @@ if (!params.skip_trimming) {`
`135`	`135`	`ext.args = {`
`136`	`136`	`[`
`137`	`137`	`'--fastqc',`
`138`		`- params.trim_nextseq > 0 ? "--nextseq ${params.trim_nextseq}" : '',`
	`138`	`+ params.trim_nextseq > 0 ? "--nextseq-trim ${params.trim_nextseq}" : '',`
`139`	`139`	`params.clip_r1 > 0 ? "--clip_r1 ${params.clip_r1}" : '',`
`140`	`140`	`params.clip_r2 > 0 ? "--clip_r2 ${params.clip_r2}" : '',`
`141`	`141`	`params.three_prime_clip_r1 > 0 ? "--three_prime_clip_r1 ${params.three_prime_clip_r1}" : '',`