From b034029b59b1198075da8019074bc02051a6100e Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Tue, 9 Aug 2022 09:18:37 +0200
Subject: [PATCH] add stub for cat/fastq (#1943)

* add stub for cat/fastq

* prettier linting
---
 modules/cat/fastq/main.nf        | 29 +++++++++++++++++++++++++++
 tests/modules/cat/fastq/test.yml | 34 ++++++++++++++++++++++++++++++++
 2 files changed, 63 insertions(+)

diff --git a/modules/cat/fastq/main.nf b/modules/cat/fastq/main.nf
index b6854895..d275f19c 100644
--- a/modules/cat/fastq/main.nf
+++ b/modules/cat/fastq/main.nf
@@ -48,4 +48,33 @@ process CAT_FASTQ {
             """
         }
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def readList = reads.collect{ it.toString() }
+    if (meta.single_end) {
+        if (readList.size > 1) {
+            """
+            touch ${prefix}.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
+            """
+        }
+    } else {
+        if (readList.size > 2) {
+            """
+            touch ${prefix}_1.merged.fastq.gz
+            touch ${prefix}_2.merged.fastq.gz
+
+            cat <<-END_VERSIONS > versions.yml
+            "${task.process}":
+                cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
+            END_VERSIONS
+            """
+        }
+    }
+
 }
diff --git a/tests/modules/cat/fastq/test.yml b/tests/modules/cat/fastq/test.yml
index 56374060..60f3eb60 100644
--- a/tests/modules/cat/fastq/test.yml
+++ b/tests/modules/cat/fastq/test.yml
@@ -37,3 +37,37 @@
       md5sum: 63f817db7a29a03eb538104495556f66
     - path: ./output/cat/test_2.merged.fastq.gz
       md5sum: fe9f266f43a6fc3dcab690a18419a56e
+
+- name: cat fastq single-end stub
+  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test.merged.fastq.gz
+
+- name: cat fastq fastqc_paired_end stub
+  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test_2.merged.fastq.gz
+    - path: ./output/cat/test_1.merged.fastq.gz
+
+- name: cat fastq single-end-same-name stub
+  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_single_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test.merged.fastq.gz
+
+- name: cat fastq fastqc_paired_end_same_name stub
+  command: nextflow run ./tests/modules/cat/fastq -entry test_cat_fastq_paired_end_same_name -c ./tests/config/nextflow.config -c ./tests/modules/cat/fastq/nextflow.config -stub-run
+  tags:
+    - cat
+    - cat/fastq
+  files:
+    - path: ./output/cat/test_1.merged.fastq.gz
+    - path: ./output/cat/test_2.merged.fastq.gz