From fed0892e5bb239db5a9c95f5a5cc401eafa1d178 Mon Sep 17 00:00:00 2001
From: Ben Sherman <bentshermann@gmail.com>
Date: Wed, 13 Dec 2023 03:36:51 -0600
Subject: [PATCH] Add missing stubs

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
---
 modules/local/gtf_filter/main.nf                    | 6 ++++++
 modules/local/multiqc/main.nf                       | 7 +++++++
 modules/nf-core/bbmap/bbsplit/main.nf               | 5 +++++
 modules/nf-core/custom/dumpsoftwareversions/main.nf | 7 +++++++
 modules/nf-core/fq/subsample/main.nf                | 6 ++++++
 modules/nf-core/salmon/quant/main.nf                | 7 +++++++
 modules/nf-core/trimgalore/main.nf                  | 6 ++++++
 7 files changed, 44 insertions(+)

diff --git a/modules/local/gtf_filter/main.nf b/modules/local/gtf_filter/main.nf
index d14e8ff42..d4b7fb613 100644
--- a/modules/local/gtf_filter/main.nf
+++ b/modules/local/gtf_filter/main.nf
@@ -29,4 +29,10 @@ process GTF_FILTER {
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch 1.filtered.gtf
+    touch versions.yml
+    """
 }
diff --git a/modules/local/multiqc/main.nf b/modules/local/multiqc/main.nf
index a59d8a533..9635a3d42 100644
--- a/modules/local/multiqc/main.nf
+++ b/modules/local/multiqc/main.nf
@@ -71,4 +71,11 @@ process MULTIQC {
         multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch 1_multiqc_report.html
+    mkdir 1_data
+    mkdir versions.yml
+    """
 }
diff --git a/modules/nf-core/bbmap/bbsplit/main.nf b/modules/nf-core/bbmap/bbsplit/main.nf
index f82bb9e47..6ca50c5ac 100644
--- a/modules/nf-core/bbmap/bbsplit/main.nf
+++ b/modules/nf-core/bbmap/bbsplit/main.nf
@@ -86,4 +86,9 @@ process BBMAP_BBSPLIT {
         END_VERSIONS
         """
     }
+
+    stub:
+    """
+    touch versions.yml
+    """
 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 7685b33cd..b1053a2c2 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -21,4 +21,11 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     script:
     def args = task.ext.args ?: ''
     template 'dumpsoftwareversions.py'
+
+    stub:
+    """
+    touch software_versions.yml
+    touch software_versions_mqc.yml
+    touch versions.yml
+    """
 }
diff --git a/modules/nf-core/fq/subsample/main.nf b/modules/nf-core/fq/subsample/main.nf
index 8b4ff5be0..702ba7877 100644
--- a/modules/nf-core/fq/subsample/main.nf
+++ b/modules/nf-core/fq/subsample/main.nf
@@ -52,4 +52,10 @@ process FQ_SUBSAMPLE {
         fq: \$(echo \$(fq subsample --version | sed 's/fq-subsample //g'))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch 1.fastq.gz
+    touch versions.yml
+    """
 }
diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf
index f11b6c2e2..ad11570a2 100644
--- a/modules/nf-core/salmon/quant/main.nf
+++ b/modules/nf-core/salmon/quant/main.nf
@@ -76,4 +76,11 @@ process SALMON_QUANT {
         salmon: \$(echo \$(salmon --version) | sed -e "s/salmon //g")
     END_VERSIONS
     """
+
+    stub:
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}
+    touch versions.yml
+    """
 }
diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf
index 24ead8714..57fc9379c 100644
--- a/modules/nf-core/trimgalore/main.nf
+++ b/modules/nf-core/trimgalore/main.nf
@@ -72,4 +72,10 @@ process TRIMGALORE {
         END_VERSIONS
         """
     }
+
+    stub:
+    """
+    touch 1_trimmed.fq.gz
+    touch versions.yml
+    """
 }