guanqiaofeng
diff --git a/‎conf/icgc-argo-workflows/modules.config
+4 b/‎conf/icgc-argo-workflows/modules.config
+4
diff --git a/‎modules.json
+14 b/‎modules.json
+14
diff --git a/‎modules/local/prep/transcript_ref/main.nf
-40 b/‎modules/local/prep/transcript_ref/main.nf
-40
diff --git a/‎modules/local/prep/transcript_ref/resources/usr/bin/gen_transcript_fa_fai.py
-72 b/‎modules/local/prep/transcript_ref/resources/usr/bin/gen_transcript_fa_fai.py
-72
diff --git a/‎modules/nf-core/gffread/environment.yml
+7 b/‎modules/nf-core/gffread/environment.yml
+7
diff --git a/‎modules/nf-core/gffread/main.nf
+60 b/‎modules/nf-core/gffread/main.nf
+60
diff --git a/‎modules/nf-core/gffread/meta.yml
+55 b/‎modules/nf-core/gffread/meta.yml
+55
@@ -94,4 +94,8 @@ process {
     withName: 'NFCORE_RNAALN:RNAALN:MERG_DUP_ST:SAMTOOLS_CONVERT' {
         ext.prefix  =  { "${meta.id}.transcriptAlign" }
     }
+    withName: 'GFFREAD' {
+        ext.args = '-w'
+        ext.prefix = 'transcript_ref'
+    }
 }
@@ -165,6 +165,13 @@
                             "modules"
                         ]
                     },
+                    "gffread": {
+                        "branch": "master",
+                        "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
                     "hisat2/align": {
                         "branch": "master",
                         "git_sha": "4eed099a12a7d586ce830a662a33a9df5bd67a24",
@@ -187,6 +194,13 @@
                         ],
                         "patch": "modules/nf-core/picard/collectrnaseqmetrics/picard-collectrnaseqmetrics.diff"
                     },
+                    "samtools/faidx": {
+                        "branch": "master",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+                        "installed_by": [
+                            "modules"
+                        ]
+                    },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
Original file line number	Diff line number	Diff line change
`@@ -94,4 +94,8 @@ process {`
`94`	`94`	`withName: 'NFCORE_RNAALN:RNAALN:MERG_DUP_ST:SAMTOOLS_CONVERT' {`
`95`	`95`	`ext.prefix = { "${meta.id}.transcriptAlign" }`
`96`	`96`	`}`
	`97`	`+ withName: 'GFFREAD' {`
	`98`	`+ ext.args = '-w'`
	`99`	`+ ext.prefix = 'transcript_ref'`
	`100`	`+ }`
`97`	`101`	`}`