Build branch main with version main (5fbd530)

Build pipeline: viash-hub.rnaseq.main-rfpzb

Source commit: 5fbd530a7c

Source message: add arguments to skip qc components

target/nextflow/bbmap_bbsplit/.config.vsh.yaml

@@ -238,8 +238,8 @@ build_info:
   output: "target/nextflow/bbmap_bbsplit"
   executable: "target/nextflow/bbmap_bbsplit/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/bbmap_bbsplit/main.nf

@@ -3104,8 +3104,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/bedtools_genomecov/.config.vsh.yaml

@@ -178,8 +178,8 @@ build_info:
   output: "target/nextflow/bedtools_genomecov"
   executable: "target/nextflow/bedtools_genomecov/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/bedtools_genomecov/main.nf

@@ -3031,8 +3031,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/cat_additional_fasta/.config.vsh.yaml

@@ -182,8 +182,8 @@ build_info:
   output: "target/nextflow/cat_additional_fasta"
   executable: "target/nextflow/cat_additional_fasta/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/cat_additional_fasta/main.nf

@@ -3032,8 +3032,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/cat_fastq/.config.vsh.yaml

@@ -169,8 +169,8 @@ build_info:
   output: "target/nextflow/cat_fastq"
   executable: "target/nextflow/cat_fastq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/cat_fastq/main.nf

@@ -3023,8 +3023,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/cat_fastq",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/deseq2_qc/.config.vsh.yaml

@@ -222,10 +222,9 @@ engines:
     - "RColorBrewer"
     - "pheatmap"
     - "stringr"
+    - "matrixStats"
     bioc:
     - "DESeq2"
-    url:
-    - "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"
     bioc_force_install: false
   entrypoint: []
   cmd: null
@@ -238,8 +237,8 @@ build_info:
   output: "target/nextflow/deseq2_qc"
   executable: "target/nextflow/deseq2_qc/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/deseq2_qc/main.nf

@@ -3083,14 +3083,12 @@ meta = [
             "ggplot2",
             "RColorBrewer",
             "pheatmap",
-            "stringr"
+            "stringr",
+            "matrixStats"
           ],
           "bioc" : [
             "DESeq2"
           ],
-          "url" : [
-            "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"
-          ],
           "bioc_force_install" : false
         }
       ]
@@ -3106,8 +3104,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/deseq2_qc",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/dupradar/.config.vsh.yaml

@@ -266,8 +266,8 @@ build_info:
   output: "target/nextflow/dupradar"
   executable: "target/nextflow/dupradar/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/dupradar/main.nf

@@ -3136,8 +3136,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/dupradar",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/fastqc/.config.vsh.yaml

@@ -198,8 +198,8 @@ build_info:
   output: "target/nextflow/fastqc"
   executable: "target/nextflow/fastqc/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/fastqc/main.nf

@@ -3056,8 +3056,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/fastqc",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/fq_subsample/.config.vsh.yaml

@@ -177,8 +177,8 @@ build_info:
   output: "target/nextflow/fq_subsample"
   executable: "target/nextflow/fq_subsample/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/fq_subsample/main.nf

@@ -3027,8 +3027,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/fq_subsample",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/getchromsizes/.config.vsh.yaml

@@ -167,8 +167,8 @@ build_info:
   output: "target/nextflow/getchromsizes"
   executable: "target/nextflow/getchromsizes/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/getchromsizes/main.nf

@@ -3013,8 +3013,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/getchromsizes",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/gtf2bed/.config.vsh.yaml

@@ -145,8 +145,8 @@ build_info:
   output: "target/nextflow/gtf2bed"
   executable: "target/nextflow/gtf2bed/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/gtf2bed/main.nf

@@ -2995,8 +2995,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gtf2bed",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/gtf_filter/.config.vsh.yaml

@@ -155,8 +155,8 @@ build_info:
   output: "target/nextflow/gtf_filter"
   executable: "target/nextflow/gtf_filter/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/gtf_filter/main.nf

@@ -3003,8 +3003,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gtf_filter",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/gunzip/.config.vsh.yaml

@@ -144,8 +144,8 @@ build_info:
   output: "target/nextflow/gunzip"
   executable: "target/nextflow/gunzip/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/gunzip/main.nf

@@ -2992,8 +2992,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/gunzip",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/kallisto/kallisto_index/.config.vsh.yaml

@@ -155,8 +155,8 @@ build_info:
   output: "target/nextflow/kallisto/kallisto_index"
   executable: "target/nextflow/kallisto/kallisto_index/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/kallisto/kallisto_index/main.nf

@@ -3002,8 +3002,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml

@@ -253,8 +253,8 @@ build_info:
   output: "target/nextflow/kallisto/kallisto_quant"
   executable: "target/nextflow/kallisto/kallisto_quant/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/kallisto/kallisto_quant/main.nf

@@ -3114,8 +3114,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/multiqc_custom_biotype/.config.vsh.yaml

@@ -161,8 +161,8 @@ build_info:
   output: "target/nextflow/multiqc_custom_biotype"
   executable: "target/nextflow/multiqc_custom_biotype/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/multiqc_custom_biotype/main.nf

@@ -3005,8 +3005,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/picard_markduplicates/.config.vsh.yaml

@@ -207,8 +207,8 @@ build_info:
   output: "target/nextflow/picard_markduplicates"
   executable: "target/nextflow/picard_markduplicates/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/picard_markduplicates/main.nf

@@ -3063,8 +3063,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/prepare_multiqc_input/.config.vsh.yaml

@@ -409,8 +409,8 @@ build_info:
   output: "target/nextflow/prepare_multiqc_input"
   executable: "target/nextflow/prepare_multiqc_input/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/prepare_multiqc_input/main.nf

@@ -3277,8 +3277,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml

@@ -138,8 +138,8 @@ build_info:
   output: "target/nextflow/preprocess_transcripts_fasta"
   executable: "target/nextflow/preprocess_transcripts_fasta/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/preprocess_transcripts_fasta/main.nf

@@ -2982,8 +2982,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/preseq_lcextrap/.config.vsh.yaml

@@ -191,8 +191,8 @@ build_info:
   output: "target/nextflow/preseq_lcextrap"
   executable: "target/nextflow/preseq_lcextrap/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/preseq_lcextrap/main.nf

@@ -3035,8 +3035,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/qualimap/.config.vsh.yaml

@@ -271,8 +271,8 @@ build_info:
   output: "target/nextflow/qualimap"
   executable: "target/nextflow/qualimap/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/qualimap/main.nf

@@ -3144,8 +3144,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/qualimap",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml

@@ -299,8 +299,8 @@ build_info:
   output: "target/nextflow/rsem/rsem_calculate_expression"
   executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rsem/rsem_calculate_expression/main.nf

@@ -3163,8 +3163,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml

@@ -182,8 +182,8 @@ build_info:
   output: "target/nextflow/rsem/rsem_merge_counts"
   executable: "target/nextflow/rsem/rsem_merge_counts/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rsem/rsem_merge_counts/main.nf

@@ -3028,8 +3028,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml

@@ -163,8 +163,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_bamstat"
   executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rseqc/rseqc_bamstat/main.nf

@@ -3016,8 +3016,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml

@@ -186,8 +186,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_inferexperiment"
   executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rseqc/rseqc_inferexperiment/main.nf

@@ -3044,8 +3044,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml

@@ -272,8 +272,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_innerdistance"
   executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rseqc/rseqc_innerdistance/main.nf

@@ -3137,8 +3137,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml

@@ -260,8 +260,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_junctionannotation"
   executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rseqc/rseqc_junctionannotation/main.nf

@@ -3128,8 +3128,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml

@@ -249,8 +249,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_junctionsaturation"
   executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rseqc/rseqc_junctionsaturation/main.nf

@@ -3113,8 +3113,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml

@@ -162,8 +162,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_readdistribution"
   executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rseqc/rseqc_readdistribution/main.nf

@@ -3017,8 +3017,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml

@@ -211,8 +211,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_readduplication"
   executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rseqc/rseqc_readduplication/main.nf

@@ -3071,8 +3071,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml

@@ -214,8 +214,8 @@ build_info:
   output: "target/nextflow/rseqc/rseqc_tin"
   executable: "target/nextflow/rseqc/rseqc_tin/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/rseqc/rseqc_tin/main.nf

@@ -3076,8 +3076,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/sortmerna/.config.vsh.yaml

@@ -192,8 +192,8 @@ build_info:
   output: "target/nextflow/sortmerna"
   executable: "target/nextflow/sortmerna/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/sortmerna/main.nf

@@ -3042,8 +3042,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/sortmerna",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/stringtie/.config.vsh.yaml

@@ -216,8 +216,8 @@ build_info:
   output: "target/nextflow/stringtie"
   executable: "target/nextflow/stringtie/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/stringtie/main.nf

@@ -3073,8 +3073,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/stringtie",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/summarizedexperiment/.config.vsh.yaml

@@ -199,8 +199,8 @@ build_info:
   output: "target/nextflow/summarizedexperiment"
   executable: "target/nextflow/summarizedexperiment/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/summarizedexperiment/main.nf

@@ -3054,8 +3054,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/trimgalore/.config.vsh.yaml

@@ -788,8 +788,8 @@ build_info:
   output: "target/nextflow/trimgalore"
   executable: "target/nextflow/trimgalore/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/trimgalore/main.nf

@@ -3576,8 +3576,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/trimgalore",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/tx2gene/.config.vsh.yaml

@@ -192,8 +192,8 @@ build_info:
   output: "target/nextflow/tx2gene"
   executable: "target/nextflow/tx2gene/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/tx2gene/main.nf

@@ -3049,8 +3049,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/tx2gene",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/tximport/.config.vsh.yaml

@@ -247,8 +247,8 @@ build_info:
   output: "target/nextflow/tximport"
   executable: "target/nextflow/tximport/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/tximport/main.nf

@@ -3114,8 +3114,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/tximport",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/ucsc/bedclip/.config.vsh.yaml

@@ -164,8 +164,8 @@ build_info:
   output: "target/nextflow/ucsc/bedclip"
   executable: "target/nextflow/ucsc/bedclip/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/ucsc/bedclip/main.nf

@@ -3018,8 +3018,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml

@@ -164,8 +164,8 @@ build_info:
   output: "target/nextflow/ucsc/bedgraphtobigwig"
   executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/ucsc/bedgraphtobigwig/main.nf

@@ -3018,8 +3018,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/umitools/umitools_dedup/.config.vsh.yaml

@@ -195,8 +195,8 @@ build_info:
   output: "target/nextflow/umitools/umitools_dedup"
   executable: "target/nextflow/umitools/umitools_dedup/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/umitools/umitools_dedup/main.nf

@@ -3054,8 +3054,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/umitools/umitools_extract/.config.vsh.yaml

@@ -253,8 +253,8 @@ build_info:
   output: "target/nextflow/umitools/umitools_extract"
   executable: "target/nextflow/umitools/umitools_extract/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/umitools/umitools_extract/main.nf

@@ -3119,8 +3119,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/umitools_prepareforquant/.config.vsh.yaml

@@ -156,8 +156,8 @@ build_info:
   output: "target/nextflow/umitools_prepareforquant"
   executable: "target/nextflow/umitools_prepareforquant/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

target/nextflow/umitools_prepareforquant/main.nf

@@ -3007,8 +3007,8 @@ meta = [
     "engine" : "docker|native",
     "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml

@@ -603,8 +603,8 @@ build_info:
   output: "target/nextflow/workflows/genome_alignment_and_quant"
   executable: "target/nextflow/workflows/genome_alignment_and_quant/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

target/nextflow/workflows/genome_alignment_and_quant/main.nf

@@ -3531,8 +3531,8 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/workflows/merge_quant_results/.config.vsh.yaml

@@ -278,8 +278,8 @@ build_info:
   output: "target/nextflow/workflows/merge_quant_results"
   executable: "target/nextflow/workflows/merge_quant_results/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/tx2gene"
   - "target/nextflow/tximport"

target/nextflow/workflows/merge_quant_results/main.nf

@@ -3149,8 +3149,8 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/workflows/post_processing/.config.vsh.yaml

@@ -486,8 +486,8 @@ build_info:
   output: "target/nextflow/workflows/post_processing"
   executable: "target/nextflow/workflows/post_processing/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/picard_markduplicates"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

target/nextflow/workflows/post_processing/main.nf

@@ -3397,8 +3397,8 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/workflows/pre_processing/.config.vsh.yaml

@@ -673,8 +673,8 @@ build_info:
   output: "target/nextflow/workflows/pre_processing"
   executable: "target/nextflow/workflows/pre_processing/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/fastqc"
   - "target/nextflow/umitools/umitools_extract"

target/nextflow/workflows/pre_processing/main.nf

@@ -3626,8 +3626,8 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/workflows/prepare_genome/.config.vsh.yaml

@@ -496,8 +496,8 @@ build_info:
   output: "target/nextflow/workflows/prepare_genome"
   executable: "target/nextflow/workflows/prepare_genome/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/gunzip"
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"

target/nextflow/workflows/prepare_genome/main.nf

@@ -3407,8 +3407,8 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml

@@ -283,8 +283,8 @@ build_info:
   output: "target/nextflow/workflows/pseudo_alignment_and_quant"
   executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
   - "target/nextflow/kallisto/kallisto_quant"

target/nextflow/workflows/pseudo_alignment_and_quant/main.nf

@@ -3143,8 +3143,8 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",

target/nextflow/workflows/quality_control/.config.vsh.yaml

@@ -213,6 +213,22 @@ argument_groups:
     direction: "input"
     multiple: false
     multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--skip_dupradar"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--skip_qualimap"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--skip_rseqc"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--skip_multiqc"
+    info: null
+    direction: "input"
   - type: "boolean"
     name: "--skip_preseq"
     info: null
@@ -1556,8 +1572,8 @@ build_info:
   output: "target/nextflow/workflows/quality_control"
   executable: "target/nextflow/workflows/quality_control/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/rseqc/rseqc_bamstat"
   - "target/nextflow/rseqc/rseqc_inferexperiment"

target/nextflow/workflows/quality_control/main.nf

@@ -3045,6 +3045,26 @@ meta = [
           "multiple" : false,
           "multiple_sep" : ";"
         },
+        {
+          "type" : "boolean_true",
+          "name" : "--skip_dupradar",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--skip_qualimap",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--skip_rseqc",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--skip_multiqc",
+          "direction" : "input"
+        },
         {
           "type" : "boolean",
           "name" : "--skip_preseq",
@@ -4628,8 +4648,8 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -4711,7 +4731,7 @@ workflow run_wf {
         }
 
         | featurecounts.run (
-            runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf },
+            runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf && !state.skip_align },
             fromState: [
                 "paired": "paired",
                 "strand": "strand", 
@@ -4732,7 +4752,7 @@ workflow run_wf {
         )
 
         | multiqc_custom_biotype.run (
-            runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts },
+            runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts && !state.skip_align },
             fromState: [
                 "id": "id",
                 "biocounts": "featurecounts", 
@@ -4745,7 +4765,7 @@ workflow run_wf {
         )
               
         | preseq_lcextrap.run (
-            runIf: { id, state -> !state.skip_qc && !state.skip_preseq },
+            runIf: { id, state -> !state.skip_qc && !state.skip_preseq && !state.skip_align },
             fromState: [
                 "paired": "paired",
                 "input": "genome_bam",
@@ -4755,7 +4775,7 @@ workflow run_wf {
         )
    
         | rseqc_bamstat.run (
-            runIf: { id, state -> "bam_stat" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "bam_stat" in state.rseqc_modules && !state.skip_align },
             fromState: [
                 "input": "genome_bam",
                 "map_qual": "map_qual"
@@ -4763,7 +4783,7 @@ workflow run_wf {
             toState: [ "bamstat_output": "output" ]
         )
         | rseqc_inferexperiment.run(
-            runIf: { id, state -> "infer_experiment" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "infer_experiment" in state.rseqc_modules && !state.skip_align },
             fromState: [
                 "input": "genome_bam",
                 "refgene": "gene_bed",
@@ -4779,7 +4799,7 @@ workflow run_wf {
             [ id, state + [ inferred_strand: inferred_strand, passed_strand_check: passed_strand_check ] ]
         }
         | rseqc_innerdistance.run(
-            runIf: { id, state -> state.paired && "inner_distance" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && state.paired && "inner_distance" in state.rseqc_modules && !state.skip_align },
             key: "inner_distance",
             fromState: [
                 "input": "genome_bam",
@@ -4799,7 +4819,7 @@ workflow run_wf {
             ]
         )
         | rseqc_junctionannotation.run(
-            runIf: { id, state -> "junction_annotation" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_annotation" in state.rseqc_modules && !state.skip_align },
             fromState: [
                 "input": "genome_bam",
                 "refgene": "gene_bed",
@@ -4817,7 +4837,7 @@ workflow run_wf {
             ]
         )
         | rseqc_junctionsaturation.run(
-            runIf: { id, state -> "junction_saturation" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_saturation" in state.rseqc_modules && !state.skip_align },
             fromState: [
                 "input": "genome_bam",
                 "refgene": "gene_bed",
@@ -4834,7 +4854,7 @@ workflow run_wf {
             ]
         )
         | rseqc_readdistribution.run(
-            runIf: { id, state -> "read_distribution" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_distribution" in state.rseqc_modules && !state.skip_align },
             fromState: [
                 "input": "genome_bam",
                 "refgene": "gene_bed", 
@@ -4842,7 +4862,7 @@ workflow run_wf {
             toState: [ "read_distribution_output": "output" ]
         )                               
         | rseqc_readduplication.run(
-            runIf: { id, state -> "read_duplication" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_duplication" in state.rseqc_modules && !state.skip_align },
             fromState: [
                 "input": "genome_bam",
                 "read_count_upper_limit": "read_count_upper_limit",
@@ -4856,7 +4876,7 @@ workflow run_wf {
             ]
         )
         | rseqc_tin.run(
-            runIf: { id, state -> "tin" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "tin" in state.rseqc_modules && !state.skip_align },
             fromState: [
                 "bam_input": "genome_bam",
                 "bai_input": "genome_bam_index",
@@ -4872,6 +4892,7 @@ workflow run_wf {
         )
 
         | dupradar.run(
+            runIf: { id, state -> !state.skip_qc && !state.skip_dupradar && !state.skip_align },
             fromState: [
                 "id": "id",
                 "input": "genome_bam",
@@ -4891,6 +4912,7 @@ workflow run_wf {
         )
 
         | qualimap.run(
+            runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align },
             fromState: [
                 "input": "genome_bam",
                 "gtf": "gtf",
@@ -4911,7 +4933,7 @@ workflow run_wf {
         
         | toSortedList
         | map { list -> 
-            def ids = list.collect { id, state -> state.id }
+            def ids = list.collect { id, state -> id }
             def strandedness = list.collect { id, state -> state.strandedness }
             def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
             def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
@@ -5217,7 +5239,7 @@ workflow run_wf {
         | deseq2_qc.run (
             runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_pseudo_align },
             fromState: [
-                "counts": "counts",
+                "counts": "pseudo_counts_gene_length_scaled",
                 "vst": "deseq2_vst", 
                 "label": "pseudo_aligner" 
             ],
@@ -5229,7 +5251,7 @@ workflow run_wf {
             ],
             key: "deseq2_qc_pseuso_align_quant"
         )
-
+        | niceView()
         // Get list of samples that failed trimming, mapping, and strand check for MultiQC report
         | map { id, state -> 
             def fail_trimming_header = ["Sample", "Reads after trimming"]
@@ -5252,7 +5274,7 @@ workflow run_wf {
                         fail_mapping_multiqc += tsv_data.join('\n')
                     }
                     if (!state.passed_strand_check[i]) {
-                        tsv_data = ([ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\t')
+                        tsv_data = ([state.ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\t')
                         fail_strand_multiqc += tsv_data.join('\n')
                     }
                 }
@@ -5272,6 +5294,7 @@ workflow run_wf {
         }
 
         | prepare_multiqc_input.run(
+            runIf: { id, state -> !state.skip_qc && !state.skip_multiqc },
             fromState: [
                 "fail_trimming_multiqc": "fail_trimming_multiqc", 
                 "fail_mapping_multiqc": "fail_mapping_multiqc", 
@@ -5312,6 +5335,7 @@ workflow run_wf {
         )
 
         | multiqc.run (
+            runIf: { id, state -> !state.skip_qc && !state.skip_multiqc },
             fromState: [
                 "title": "multiqc_title", 
                 "input": "multiqc_input", 

target/nextflow/workflows/quality_control/nextflow_schema.json

@@ -238,6 +238,50 @@
             }
     
 
+        ,
+                "skip_dupradar": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. ",
+                "help_text": "Type: `boolean_true`, default: `false`. "
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "skip_qualimap": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. ",
+                "help_text": "Type: `boolean_true`, default: `false`. "
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "skip_rseqc": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. ",
+                "help_text": "Type: `boolean_true`, default: `false`. "
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "skip_multiqc": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. ",
+                "help_text": "Type: `boolean_true`, default: `false`. "
+            ,
+                "default": "False"
+            }
+    
+
         ,
                 "skip_preseq": {
                 "type":

target/nextflow/workflows/rnaseq/.config.vsh.yaml

@@ -607,17 +607,22 @@ argument_groups:
     info: null
     direction: "input"
   - type: "boolean_true"
-    name: "skip_dupradar"
+    name: "--skip_dupradar"
     description: "Skip dupRadar."
     info: null
     direction: "input"
   - type: "boolean_true"
-    name: "skip_rseqc"
+    name: "--skip_qualimap"
+    description: "Skip Qualimap."
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--skip_rseqc"
     description: "Skip RSeQC."
     info: null
     direction: "input"
   - type: "boolean_true"
-    name: "skip_multiqc"
+    name: "--skip_multiqc"
     description: "Skip MultiQC."
     info: null
     direction: "input"
@@ -2077,8 +2082,8 @@ build_info:
   output: "target/nextflow/workflows/rnaseq"
   executable: "target/nextflow/workflows/rnaseq/main.nf"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/workflows/prepare_genome"
   - "target/nextflow/cat_fastq"

target/nextflow/workflows/rnaseq/main.nf

@@ -3492,19 +3492,25 @@ meta = [
         },
         {
           "type" : "boolean_true",
-          "name" : "skip_dupradar",
+          "name" : "--skip_dupradar",
           "description" : "Skip dupRadar.",
           "direction" : "input"
         },
         {
           "type" : "boolean_true",
-          "name" : "skip_rseqc",
+          "name" : "--skip_qualimap",
+          "description" : "Skip Qualimap.",
+          "direction" : "input"
+        },
+        {
+          "type" : "boolean_true",
+          "name" : "--skip_rseqc",
           "description" : "Skip RSeQC.",
           "direction" : "input"
         },
         {
           "type" : "boolean_true",
-          "name" : "skip_multiqc",
+          "name" : "--skip_multiqc",
           "description" : "Skip MultiQC.",
           "direction" : "input"
         }
@@ -4879,12 +4885,12 @@ meta = [
           "required" : false,
           "direction" : "output",
           "multiple" : false,
-          "multiple_sep" : ";"
+    ''' + '''      "multiple_sep" : ";"
         },
         {
           "type" : "file",
           "name" : "--dupradar_output_expression_histogram",
-          "description" : "path to outpu''' + '''t file (pdf) of distribution of RPK values per gene histogram",
+          "description" : "path to output file (pdf) of distribution of RPK values per gene histogram",
           "default" : [
             "dupradar/histogram/$id.expression_hist.pdf"
           ],
@@ -5236,8 +5242,8 @@ meta = [
     "engine" : "native",
     "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq",
     "viash_version" : "0.9.0",
-    "git_commit" : "05d48ac2f802e6510893b0966727b56adf2d5bf7",
-    "git_remote" : "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+    "git_commit" : "5fbd530a7cf631bcc2930747d4712993ee19f07a",
+    "git_remote" : "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
   },
   "package_config" : {
     "name" : "rnaseq",
@@ -5533,7 +5539,7 @@ workflow run_wf {
 
     // Filter channels to get samples that passed STAR minimum mapping percentage
     | map { id, state -> 
-      def percent_mapped = getStarPercentMapped(state.star_multiqc) 
+      def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0
       def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false
       [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ]
     }
@@ -5628,6 +5634,11 @@ workflow run_wf {
           "strandedness": "strandedness", 
           "skip_align": "skip_alignment",
           "skip_pseudo_align": "skip_pseudo_alignment",
+          "skip_dupradar": "skip_dupradar",
+          "skip_qualimap": "skip_qualimap",
+          "skip_rseqc": "skip_rseqc",
+          "skip_multiqc": "skip_multiqc",
+          "skip_preseq": "skip_preseq",
           "gtf": "gtf", 
           "num_trimmed_reads": "num_trimmed_reads",
           "passed_trimmed_reads": "passed_trimmed_reads",

target/nextflow/workflows/rnaseq/nextflow_schema.json

@@ -768,6 +768,17 @@
             }
     
 
+        ,
+                "skip_qualimap": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Skip Qualimap",
+                "help_text": "Type: `boolean_true`, default: `false`. Skip Qualimap."
+            ,
+                "default": "False"
+            }
+    
+
         ,
                 "skip_rseqc": {
                 "type":