From a5a6973fcf161d0449b216c166ba232c6c55bcbb Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Sat, 21 May 2022 08:33:49 +0200
Subject: [PATCH 1/6] picard: make reference sequence optional

---
 modules/picard/collecthsmetrics/main.nf       | 2 +-
 modules/picard/collectmultiplemetrics/main.nf | 3 ++-
 modules/picard/collectwgsmetrics/main.nf      | 3 ++-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/picard/collecthsmetrics/main.nf b/modules/picard/collecthsmetrics/main.nf
index 317aff4b..06b6b8f3 100644
--- a/modules/picard/collecthsmetrics/main.nf
+++ b/modules/picard/collecthsmetrics/main.nf
@@ -24,7 +24,7 @@ process PICARD_COLLECTHSMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "-R $fasta" : ""
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
 
     def avail_mem = 3
     if (!task.memory) {
diff --git a/modules/picard/collectmultiplemetrics/main.nf b/modules/picard/collectmultiplemetrics/main.nf
index a653b549..3c3152df 100644
--- a/modules/picard/collectmultiplemetrics/main.nf
+++ b/modules/picard/collectmultiplemetrics/main.nf
@@ -22,6 +22,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard CollectMultipleMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -35,7 +36,7 @@ process PICARD_COLLECTMULTIPLEMETRICS {
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.CollectMultipleMetrics \\
-        --REFERENCE_SEQUENCE $fasta
+        $reference
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index e6dd49e9..13446fcf 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -21,6 +21,7 @@ process PICARD_COLLECTWGSMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -34,7 +35,7 @@ process PICARD_COLLECTWGSMETRICS {
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
-        --REFERENCE_SEQUENCE $fasta
+        $reference
 
 
     cat <<-END_VERSIONS > versions.yml

From 4da143ce62dfcfbe7b23394be0ae5520a442b43b Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Sun, 22 May 2022 06:43:48 +0200
Subject: [PATCH 2/6] add tests

---
 tests/modules/picard/collecthsmetrics/main.nf | 11 ++++
 .../modules/picard/collecthsmetrics/test.yml  | 15 ++++-
 .../picard/collectmultiplemetrics/main.nf     | 14 ++++-
 .../picard/collectmultiplemetrics/test.yml    | 62 +++++++++++++++----
 4 files changed, 84 insertions(+), 18 deletions(-)

diff --git a/tests/modules/picard/collecthsmetrics/main.nf b/tests/modules/picard/collecthsmetrics/main.nf
index a28eb174..b25f3bf5 100644
--- a/tests/modules/picard/collecthsmetrics/main.nf
+++ b/tests/modules/picard/collecthsmetrics/main.nf
@@ -16,3 +16,14 @@ workflow test_picard_collecthsmetrics {
 
     PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals )
 }
+
+workflow test_picard_collecthsmetrics_nofasta {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+
+    bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
+    target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
+
+    PICARD_COLLECTHSMETRICS ( input, [], [], bait_intervals, target_intervals )
+}
diff --git a/tests/modules/picard/collecthsmetrics/test.yml b/tests/modules/picard/collecthsmetrics/test.yml
index 9aa14f15..547cc09f 100644
--- a/tests/modules/picard/collecthsmetrics/test.yml
+++ b/tests/modules/picard/collecthsmetrics/test.yml
@@ -1,8 +1,17 @@
 - name: picard collecthsmetrics test_picard_collecthsmetrics
-  command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config
+  command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collecthsmetrics/nextflow.config
   tags:
-    - picard
     - picard/collecthsmetrics
+    - picard
   files:
-    # The file can't be md5'd consistently
     - path: output/picard/test.CollectHsMetrics.coverage_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+
+- name: picard collecthsmetrics test_picard_collecthsmetrics_nofasta
+  command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collecthsmetrics/nextflow.config
+  tags:
+    - picard/collecthsmetrics
+    - picard
+  files:
+    - path: output/picard/test.CollectHsMetrics.coverage_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
diff --git a/tests/modules/picard/collectmultiplemetrics/main.nf b/tests/modules/picard/collectmultiplemetrics/main.nf
index 453ecc91..4fee5f73 100644
--- a/tests/modules/picard/collectmultiplemetrics/main.nf
+++ b/tests/modules/picard/collectmultiplemetrics/main.nf
@@ -5,10 +5,20 @@ nextflow.enable.dsl = 2
 include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf'
 
 workflow test_picard_collectmultiplemetrics {
-    input = [ [ id:'test', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+    input = [
+                [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     PICARD_COLLECTMULTIPLEMETRICS ( input, fasta )
 }
+
+workflow test_picard_collectmultiplemetrics_nofasta {
+    input = [
+                [ id:'test', single_end:false ], // meta map
+                file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
+            ]
+
+    PICARD_COLLECTMULTIPLEMETRICS ( input, [] )
+}
diff --git a/tests/modules/picard/collectmultiplemetrics/test.yml b/tests/modules/picard/collectmultiplemetrics/test.yml
index 8fecca73..db77a585 100644
--- a/tests/modules/picard/collectmultiplemetrics/test.yml
+++ b/tests/modules/picard/collectmultiplemetrics/test.yml
@@ -1,17 +1,53 @@
-- name: picard collectmultiplemetrics
-  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
+- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics
+  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
   tags:
     - picard
     - picard/collectmultiplemetrics
   files:
-    # These can't be md5'd consistently
-    - path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-    - path: ./output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+
+- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
+  command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
+  tags:
+    - picard
+    - picard/collectmultiplemetrics
+  files:
+    - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
+    - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'

From c390385cf5a234906a30f013ba0a3c9a27b1b601 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Sun, 22 May 2022 06:44:05 +0200
Subject: [PATCH 3/6] revert wgsmetrics'

---
 modules/picard/collectwgsmetrics/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/picard/collectwgsmetrics/main.nf b/modules/picard/collectwgsmetrics/main.nf
index 13446fcf..cab1fe0c 100644
--- a/modules/picard/collectwgsmetrics/main.nf
+++ b/modules/picard/collectwgsmetrics/main.nf
@@ -21,7 +21,6 @@ process PICARD_COLLECTWGSMETRICS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reference = fasta ? "--REFERENCE_SEQUENCE ${fasta}" : ""
     def avail_mem = 3
     if (!task.memory) {
         log.info '[Picard CollectWgsMetrics] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -35,7 +34,7 @@ process PICARD_COLLECTWGSMETRICS {
         $args \\
         --INPUT $bam \\
         --OUTPUT ${prefix}.CollectWgsMetrics.coverage_metrics \\
-        $reference
+        --REFERENCE_SEQUENCE ${fasta}
 
 
     cat <<-END_VERSIONS > versions.yml

From 3a2de0cf6f670a5652d3b3d961fcf25b6fc3cc03 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Sun, 22 May 2022 06:49:31 +0200
Subject: [PATCH 4/6] update test for wgsmetrics

---
 tests/modules/picard/collectwgsmetrics/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/picard/collectwgsmetrics/test.yml b/tests/modules/picard/collectwgsmetrics/test.yml
index 2daef406..72a017da 100644
--- a/tests/modules/picard/collectwgsmetrics/test.yml
+++ b/tests/modules/picard/collectwgsmetrics/test.yml
@@ -1,5 +1,5 @@
 - name: picard collectwgsmetrics test_picard_collectwgsmetrics
-  command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectwgsmetrics/nextflow.config
+  command: nextflow run ./tests/modules/picard/collectwgsmetrics -entry test_picard_collectwgsmetrics -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectwgsmetrics/nextflow.config
   tags:
     - picard/collectwgsmetrics
     - picard

From cbceee9621e0c1fcaf50c77a01ce2345e469d22b Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Sun, 22 May 2022 06:51:27 +0200
Subject: [PATCH 5/6] fix tests

---
 tests/modules/picard/collecthsmetrics/test.yml       |  2 --
 tests/modules/picard/collectmultiplemetrics/test.yml | 10 ----------
 tests/modules/picard/collectwgsmetrics/test.yml      |  5 +----
 3 files changed, 1 insertion(+), 16 deletions(-)

diff --git a/tests/modules/picard/collecthsmetrics/test.yml b/tests/modules/picard/collecthsmetrics/test.yml
index 547cc09f..61069b55 100644
--- a/tests/modules/picard/collecthsmetrics/test.yml
+++ b/tests/modules/picard/collecthsmetrics/test.yml
@@ -5,7 +5,6 @@
     - picard
   files:
     - path: output/picard/test.CollectHsMetrics.coverage_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
 
 - name: picard collecthsmetrics test_picard_collecthsmetrics_nofasta
   command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collecthsmetrics/nextflow.config
@@ -14,4 +13,3 @@
     - picard
   files:
     - path: output/picard/test.CollectHsMetrics.coverage_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
diff --git a/tests/modules/picard/collectmultiplemetrics/test.yml b/tests/modules/picard/collectmultiplemetrics/test.yml
index db77a585..faa002b6 100644
--- a/tests/modules/picard/collectmultiplemetrics/test.yml
+++ b/tests/modules/picard/collectmultiplemetrics/test.yml
@@ -32,22 +32,12 @@
     - picard/collectmultiplemetrics
   files:
     - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
diff --git a/tests/modules/picard/collectwgsmetrics/test.yml b/tests/modules/picard/collectwgsmetrics/test.yml
index 72a017da..8cfeb43a 100644
--- a/tests/modules/picard/collectwgsmetrics/test.yml
+++ b/tests/modules/picard/collectwgsmetrics/test.yml
@@ -5,7 +5,4 @@
     - picard
   files:
     - path: output/picard/test.CollectWgsMetrics.coverage_metrics
-      contains:
-        - "GENOME_TERRITORY"
-        - "29829"
-        - "17554"
+      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'

From e13fbf423e2993d15fb882fc85097993688d2b19 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Sun, 22 May 2022 06:54:09 +0200
Subject: [PATCH 6/6] fix tests (again)

---
 tests/modules/picard/collectmultiplemetrics/test.yml | 10 ----------
 tests/modules/picard/collectwgsmetrics/test.yml      |  1 -
 2 files changed, 11 deletions(-)

diff --git a/tests/modules/picard/collectmultiplemetrics/test.yml b/tests/modules/picard/collectmultiplemetrics/test.yml
index faa002b6..475778fe 100644
--- a/tests/modules/picard/collectmultiplemetrics/test.yml
+++ b/tests/modules/picard/collectmultiplemetrics/test.yml
@@ -5,25 +5,15 @@
     - picard/collectmultiplemetrics
   files:
     - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
     - path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
 
 - name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
   command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config  -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
diff --git a/tests/modules/picard/collectwgsmetrics/test.yml b/tests/modules/picard/collectwgsmetrics/test.yml
index 8cfeb43a..6e99a04c 100644
--- a/tests/modules/picard/collectwgsmetrics/test.yml
+++ b/tests/modules/picard/collectwgsmetrics/test.yml
@@ -5,4 +5,3 @@
     - picard
   files:
     - path: output/picard/test.CollectWgsMetrics.coverage_metrics
-      contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'