From 723852bf3d3b12059b2f53da8bc055206f3019d7 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 31 May 2022 13:38:18 +0200
Subject: [PATCH 1/2] Fixes running without shortreads, and also ensures all
 tests produce non-empty fastq.gz files

---
 modules/filtlong/main.nf               |  2 +-
 tests/modules/filtlong/nextflow.config |  2 ++
 tests/modules/filtlong/test.yml        | 12 ++++++------
 3 files changed, 9 insertions(+), 7 deletions(-)

diff --git a/modules/filtlong/main.nf b/modules/filtlong/main.nf
index 0e6fdd53..67500053 100644
--- a/modules/filtlong/main.nf
+++ b/modules/filtlong/main.nf
@@ -20,7 +20,7 @@ process FILTLONG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
+    def short_reads = !shortreads ? "" : meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
     """
     filtlong \\
         $short_reads \\
diff --git a/tests/modules/filtlong/nextflow.config b/tests/modules/filtlong/nextflow.config
index 8730f1c4..ec9854c2 100644
--- a/tests/modules/filtlong/nextflow.config
+++ b/tests/modules/filtlong/nextflow.config
@@ -2,4 +2,6 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    ext.args = "--min_length 10"
+
 }
diff --git a/tests/modules/filtlong/test.yml b/tests/modules/filtlong/test.yml
index dc5fa5a9..9c465303 100644
--- a/tests/modules/filtlong/test.yml
+++ b/tests/modules/filtlong/test.yml
@@ -1,23 +1,23 @@
 - name: filtlong test_filtlong
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
+  command: nextflow run ./tests/modules/filtlong -entry test_filtlong -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
   tags:
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      md5sum: ff2b6e10fea0c45f10e8739a5bca25ed
 
 - name: filtlong test_filtlong_illumina_se
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
+  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
   tags:
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      md5sum: ff2b6e10fea0c45f10e8739a5bca25ed
 
 - name: filtlong test_filtlong_illumina_pe
-  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config -c ./tests/modules/filtlong/nextflow.config
+  command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
   tags:
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: 7029066c27ac6f5ef18d660d5741979a
+      md5sum: ff2b6e10fea0c45f10e8739a5bca25ed

From 430def06faabbbbfe03da68661c329b85a1296ed Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 31 May 2022 14:45:41 +0200
Subject: [PATCH 2/2] Switch from md5sum to string due to conda flakiness

---
 tests/modules/filtlong/test.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/tests/modules/filtlong/test.yml b/tests/modules/filtlong/test.yml
index 9c465303..93f847ec 100644
--- a/tests/modules/filtlong/test.yml
+++ b/tests/modules/filtlong/test.yml
@@ -4,7 +4,8 @@
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: ff2b6e10fea0c45f10e8739a5bca25ed
+      contains:
+        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
 
 - name: filtlong test_filtlong_illumina_se
   command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_se -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
@@ -12,7 +13,8 @@
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: ff2b6e10fea0c45f10e8739a5bca25ed
+      contains:
+        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"
 
 - name: filtlong test_filtlong_illumina_pe
   command: nextflow run ./tests/modules/filtlong -entry test_filtlong_illumina_pe -c ./tests/config/nextflow.config  -c ./tests/modules/filtlong/nextflow.config
@@ -20,4 +22,5 @@
     - filtlong
   files:
     - path: output/filtlong/test_lr_filtlong.fastq.gz
-      md5sum: ff2b6e10fea0c45f10e8739a5bca25ed
+      contains:
+        - "@00068f7a-51b3-4933-8fc6-7d6e29181ff9"