From 67c1bc9568cfc40cf7038c7be13b976fe76d76a1 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Fri, 1 Apr 2022 17:35:15 +0200
Subject: [PATCH] Add stubs to cnvpytor module (#1473)

* callcnvs stub and tests

* partition stub and test

* histogram stub and test

* importreaddepth stub and tests

* update module scripts

Co-authored-by: Sima Rahimi <sima.rahimi@gu.se>
---
 modules/cnvpytor/callcnvs/main.nf             | 11 ++++++
 modules/cnvpytor/histogram/main.nf            | 10 +++++
 modules/cnvpytor/importreaddepth/main.nf      | 11 ++++++
 modules/cnvpytor/partition/main.nf            | 12 +++++-
 tests/modules/cnvpytor/callcnvs/test.yml      | 14 ++++++-
 tests/modules/cnvpytor/histogram/test.yml     | 12 +++++-
 .../cnvpytor/importreaddepth/nextflow.config  |  2 +-
 .../modules/cnvpytor/importreaddepth/test.yml | 39 +++++++++++++++++++
 tests/modules/cnvpytor/partition/test.yml     | 12 +++++-
 9 files changed, 117 insertions(+), 6 deletions(-)
 create mode 100644 tests/modules/cnvpytor/importreaddepth/test.yml

diff --git a/modules/cnvpytor/callcnvs/main.nf b/modules/cnvpytor/callcnvs/main.nf
index e296656b..17675cde 100644
--- a/modules/cnvpytor/callcnvs/main.nf
+++ b/modules/cnvpytor/callcnvs/main.nf
@@ -30,4 +30,15 @@ process CNVPYTOR_CALLCNVS {
         cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }
diff --git a/modules/cnvpytor/histogram/main.nf b/modules/cnvpytor/histogram/main.nf
index e421f1b2..d1c6856c 100644
--- a/modules/cnvpytor/histogram/main.nf
+++ b/modules/cnvpytor/histogram/main.nf
@@ -29,4 +29,14 @@ process CNVPYTOR_HISTOGRAM {
         cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch test.pytor
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }
diff --git a/modules/cnvpytor/importreaddepth/main.nf b/modules/cnvpytor/importreaddepth/main.nf
index 1b037629..162da719 100644
--- a/modules/cnvpytor/importreaddepth/main.nf
+++ b/modules/cnvpytor/importreaddepth/main.nf
@@ -35,4 +35,15 @@ process CNVPYTOR_IMPORTREADDEPTH {
         cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.pytor
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }
diff --git a/modules/cnvpytor/partition/main.nf b/modules/cnvpytor/partition/main.nf
index 74ab4026..975458bf 100644
--- a/modules/cnvpytor/partition/main.nf
+++ b/modules/cnvpytor/partition/main.nf
@@ -18,7 +18,7 @@ process CNVPYTOR_PARTITION {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: '1000'
+    def args = task.ext.args ?: ''
     """
     cnvpytor \\
         -root $pytor \\
@@ -29,4 +29,14 @@ process CNVPYTOR_PARTITION {
         cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch test.pytor
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
 }
diff --git a/tests/modules/cnvpytor/callcnvs/test.yml b/tests/modules/cnvpytor/callcnvs/test.yml
index 85bfcc7a..4565151e 100644
--- a/tests/modules/cnvpytor/callcnvs/test.yml
+++ b/tests/modules/cnvpytor/callcnvs/test.yml
@@ -4,7 +4,17 @@
     - cnvpytor
     - cnvpytor/callcnvs
   files:
-    - path: output/cnvpytor/calls.10000.tsv
+    - path: output/cnvpytor/test.tsv
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cnvpytor/versions.yml
-      md5sum: 5fe6ca3ef5c40f9dbf487f28db237821
+      md5sum: 0bea08a253fcb2ff0ff79b99df77b9fa
+
+- name: cnvpytor callcnvs test_cnvpytor_callcnvs stub
+  command: nextflow run tests/modules/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/callcnvs
+  files:
+    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/versions.yml
+      md5sum: 0bea08a253fcb2ff0ff79b99df77b9fa
diff --git a/tests/modules/cnvpytor/histogram/test.yml b/tests/modules/cnvpytor/histogram/test.yml
index fd8bcaf4..0543fcc3 100644
--- a/tests/modules/cnvpytor/histogram/test.yml
+++ b/tests/modules/cnvpytor/histogram/test.yml
@@ -7,4 +7,14 @@
     - path: output/cnvpytor/test.pytor
       md5sum: aa03a8fa15b39f77816705a48e10312a
     - path: output/cnvpytor/versions.yml
-      md5sum: 9a4b176afd5f1a3edeb37eeb301cf464
+      md5sum: 0f4d75c4f3a3eb26c22616d12b0b78b2
+
+- name: cnvpytor histogram test_cnvpytor_histogram stub
+  command: nextflow run tests/modules/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/histogram
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: 0f4d75c4f3a3eb26c22616d12b0b78b2
diff --git a/tests/modules/cnvpytor/importreaddepth/nextflow.config b/tests/modules/cnvpytor/importreaddepth/nextflow.config
index c60f979e..4383e375 100644
--- a/tests/modules/cnvpytor/importreaddepth/nextflow.config
+++ b/tests/modules/cnvpytor/importreaddepth/nextflow.config
@@ -8,5 +8,5 @@ process {
 }
 
 params {
-    cnvpytor_chr = '' // specifies chromosome name(s) the same way as they are described in the sam/bam/cram header e.g. '1 2' or 'chr1 chr2'.
+    cnvpytor_chr = null // specifies chromosome name(s) the same way as they are described in the sam/bam/cram header e.g. '1 2' or 'chr1 chr2'.
     }
diff --git a/tests/modules/cnvpytor/importreaddepth/test.yml b/tests/modules/cnvpytor/importreaddepth/test.yml
new file mode 100644
index 00000000..b148c38e
--- /dev/null
+++ b/tests/modules/cnvpytor/importreaddepth/test.yml
@@ -0,0 +1,39 @@
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth
+  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: 5834495324c08a37f3fd73ccdd881dc8
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth stub
+  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: 5834495324c08a37f3fd73ccdd881dc8
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram
+  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: dfa0afb0982d985b96d1633f71ebb82a
+
+- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram stub
+  command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/importreaddepth
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: dfa0afb0982d985b96d1633f71ebb82a
diff --git a/tests/modules/cnvpytor/partition/test.yml b/tests/modules/cnvpytor/partition/test.yml
index 1b838395..10232097 100644
--- a/tests/modules/cnvpytor/partition/test.yml
+++ b/tests/modules/cnvpytor/partition/test.yml
@@ -7,4 +7,14 @@
     - path: output/cnvpytor/test.pytor
       md5sum: aa03a8fa15b39f77816705a48e10312a
     - path: output/cnvpytor/versions.yml
-      md5sum: 8a04506554c58cd170cc050fd9904c6f
+      md5sum: 7fd6ec952a316463bcd324f176b46b64
+
+- name: cnvpytor partition test_cnvpytor_partition stub
+  command: nextflow run tests/modules/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/partition
+  files:
+    - path: output/cnvpytor/test.pytor
+    - path: output/cnvpytor/versions.yml
+      md5sum: 7fd6ec952a316463bcd324f176b46b64