From bad832c2ea8af993e6f43bfa76c6c7307485f195 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Fri, 29 Apr 2022 14:28:45 +0200
Subject: [PATCH 01/21] Add Sexdeterrmine module

---
 modules/sexdeterrmine/main.nf               | 38 ++++++++++++++++
 modules/sexdeterrmine/meta.yml              | 48 +++++++++++++++++++++
 tests/config/pytest_modules.yml             |  4 ++
 tests/modules/sexdeterrmine/main.nf         | 16 +++++++
 tests/modules/sexdeterrmine/nextflow.config |  8 ++++
 tests/modules/sexdeterrmine/test.yml        | 12 ++++++
 6 files changed, 126 insertions(+)
 create mode 100644 modules/sexdeterrmine/main.nf
 create mode 100644 modules/sexdeterrmine/meta.yml
 create mode 100644 tests/modules/sexdeterrmine/main.nf
 create mode 100644 tests/modules/sexdeterrmine/nextflow.config
 create mode 100644 tests/modules/sexdeterrmine/test.yml

diff --git a/modules/sexdeterrmine/main.nf b/modules/sexdeterrmine/main.nf
new file mode 100644
index 00000000..f8754764
--- /dev/null
+++ b/modules/sexdeterrmine/main.nf
@@ -0,0 +1,38 @@
+process SEXDETERRMINE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/sexdeterrmine:1.1.2--hdfd78af_1':
+        'quay.io/biocontainers/sexdeterrmine:1.1.2--hdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(depth)
+    path(sample_list_file)
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    tuple val(meta), path("*.tsv") , emit: tsv
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
+    """
+    sexdeterrmine \\
+        -I $depth \\
+        $sample_list \\
+        $args \\
+        > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sexdeterrmine: \$(echo \$(sexdeterrmine --version 2>&1))
+    END_VERSIONS
+    """
+}
diff --git a/modules/sexdeterrmine/meta.yml b/modules/sexdeterrmine/meta.yml
new file mode 100644
index 00000000..6e24c817
--- /dev/null
+++ b/modules/sexdeterrmine/meta.yml
@@ -0,0 +1,48 @@
+name: "sexdeterrmine"
+description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
+keywords:
+  - "sex determination"
+  - "genetic sex"
+  - "relative coverage"
+tools:
+  - "sexdeterrmine":
+      description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data."
+      homepage: "https://github.com/TCLamnidis/Sex.DetERRmine"
+      documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md"
+      tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine"
+      doi: "https://doi.org/10.1038/s41467-018-07483-5"
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  #
+  - depth:
+      type: file
+      description: output from samtools depth (with header)
+      pattern: "*"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - json:
+      type: file
+      description: JSON formatted table of relative coverages on the X and Y, with associated error bars.
+      pattern: "*.json"
+  - tsv:
+      type: file
+      description: TSV table of relative coverages on the X and Y, with associated error bars.
+      pattern: "*.tsv"
+
+authors:
+  - "@TCLamnidis"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index a1a969e7..60c2d46d 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1703,6 +1703,10 @@ seqwish/induce:
   - modules/seqwish/induce/**
   - tests/modules/seqwish/induce/**
 
+sexdeterrmine:
+  - modules/sexdeterrmine/**
+  - tests/modules/sexdeterrmine/**
+
 shovill:
   - modules/shovill/**
   - tests/modules/shovill/**
diff --git a/tests/modules/sexdeterrmine/main.nf b/tests/modules/sexdeterrmine/main.nf
new file mode 100644
index 00000000..c9d869f5
--- /dev/null
+++ b/tests/modules/sexdeterrmine/main.nf
@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SAMTOOLS_DEPTH } from '../../../modules/samtools/depth/main.nf'
+include { SEXDETERRMINE } from '../../../modules/sexdeterrmine/main.nf'
+
+workflow test_sexdeterrmine {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) ]
+
+    SAMTOOLS_DEPTH ( input )
+    SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
+}
diff --git a/tests/modules/sexdeterrmine/nextflow.config b/tests/modules/sexdeterrmine/nextflow.config
new file mode 100644
index 00000000..763d7ad6
--- /dev/null
+++ b/tests/modules/sexdeterrmine/nextflow.config
@@ -0,0 +1,8 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName:SAMTOOLS_DEPTH {
+        ext.args = "-aa -H"
+    }
+}
diff --git a/tests/modules/sexdeterrmine/test.yml b/tests/modules/sexdeterrmine/test.yml
new file mode 100644
index 00000000..5eca8a30
--- /dev/null
+++ b/tests/modules/sexdeterrmine/test.yml
@@ -0,0 +1,12 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml sexdeterrmine
+- name: "sexdeterrmine"
+  command: nextflow run ./tests/modules/sexdeterrmine -entry test_sexdeterrmine -c ./tests/config/nextflow.config -c ./tests/modules/sexdeterrmine/nextflow.config
+  tags:
+    - "sexdeterrmine"
+    #
+  files:
+    - path: "output/sexdeterrmine/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/sexdeterrmine/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b

From 4317ad85aede53086cdb1ac2410a46e85e00bed4 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Fri, 29 Apr 2022 15:07:32 +0200
Subject: [PATCH 02/21] Passing test

---
 modules/sexdeterrmine/main.nf               |  2 ++
 tests/modules/sexdeterrmine/main.nf         |  2 +-
 tests/modules/sexdeterrmine/nextflow.config |  6 +++++-
 tests/modules/sexdeterrmine/test.yml        | 21 ++++++++++++---------
 4 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/modules/sexdeterrmine/main.nf b/modules/sexdeterrmine/main.nf
index f8754764..dd8b5a70 100644
--- a/modules/sexdeterrmine/main.nf
+++ b/modules/sexdeterrmine/main.nf
@@ -23,6 +23,8 @@ process SEXDETERRMINE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
+    if ("$depth" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     """
     sexdeterrmine \\
         -I $depth \\
diff --git a/tests/modules/sexdeterrmine/main.nf b/tests/modules/sexdeterrmine/main.nf
index c9d869f5..2c90d280 100644
--- a/tests/modules/sexdeterrmine/main.nf
+++ b/tests/modules/sexdeterrmine/main.nf
@@ -9,7 +9,7 @@ workflow test_sexdeterrmine {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true) ]
+        file("https://github.com/nf-core/test-datasets/raw/eager/testdata/Human/bam/JK2067_downsampled_s0.1.bam", checkIfExists: true) ]
 
     SAMTOOLS_DEPTH ( input )
     SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
diff --git a/tests/modules/sexdeterrmine/nextflow.config b/tests/modules/sexdeterrmine/nextflow.config
index 763d7ad6..4ba3dfe3 100644
--- a/tests/modules/sexdeterrmine/nextflow.config
+++ b/tests/modules/sexdeterrmine/nextflow.config
@@ -3,6 +3,10 @@ process {
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
     withName:SAMTOOLS_DEPTH {
-        ext.args = "-aa -H"
+        ext.args = "-H"
+    }
+
+    withName:SEXDETERRMINE {
+        ext.prefix = { "${meta.id}_sexdet" }
     }
 }
diff --git a/tests/modules/sexdeterrmine/test.yml b/tests/modules/sexdeterrmine/test.yml
index 5eca8a30..54c471ba 100644
--- a/tests/modules/sexdeterrmine/test.yml
+++ b/tests/modules/sexdeterrmine/test.yml
@@ -1,12 +1,15 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml sexdeterrmine
-- name: "sexdeterrmine"
-  command: nextflow run ./tests/modules/sexdeterrmine -entry test_sexdeterrmine -c ./tests/config/nextflow.config -c ./tests/modules/sexdeterrmine/nextflow.config
+- name: sexdeterrmine test_sexdeterrmine
+  command: nextflow run tests/modules/sexdeterrmine -entry test_sexdeterrmine -c tests/config/nextflow.config
   tags:
-    - "sexdeterrmine"
-    #
+    - sexdeterrmine
   files:
-    - path: "output/sexdeterrmine/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/samtools/test.tsv
+      md5sum: c894abd0c78ea7760e0b54bbafb93722
+    - path: output/samtools/versions.yml
+      md5sum: dbd04b700335c8ad236bd667254c8dd8
+    - path: output/sexdeterrmine/sexdeterrmine.json
+      md5sum: 16d9e7891d4c92bc1d66db2e70e9d86f
+    - path: output/sexdeterrmine/test_sexdet.tsv
+      md5sum: 7ffc35e478de66939819a9ca4a5df2d7
     - path: output/sexdeterrmine/versions.yml
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+      md5sum: 077361101e8e7997aec3da8a01e59eee

From 070dee0f5bef37951493cf02dfec4c22472010d4 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Mon, 23 May 2022 15:22:22 +0200
Subject: [PATCH 03/21] Use newly added test bam

---
 tests/modules/sexdeterrmine/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/sexdeterrmine/main.nf b/tests/modules/sexdeterrmine/main.nf
index 2c90d280..056c63d5 100644
--- a/tests/modules/sexdeterrmine/main.nf
+++ b/tests/modules/sexdeterrmine/main.nf
@@ -9,7 +9,7 @@ workflow test_sexdeterrmine {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file("https://github.com/nf-core/test-datasets/raw/eager/testdata/Human/bam/JK2067_downsampled_s0.1.bam", checkIfExists: true) ]
+        file(params.test_data['homo_sapiens']['illumina']['test3.single_end.markduplicates.sorted.bam'], checkIfExists: true) ]
 
     SAMTOOLS_DEPTH ( input )
     SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )

From 9011fc7212ba3889792b5026e883e2f60c714028 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Mon, 23 May 2022 17:08:40 +0200
Subject: [PATCH 04/21] Corrected test-datasets input

---
 tests/modules/sexdeterrmine/main.nf  | 2 +-
 tests/modules/sexdeterrmine/test.yml | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/modules/sexdeterrmine/main.nf b/tests/modules/sexdeterrmine/main.nf
index 056c63d5..fc777905 100644
--- a/tests/modules/sexdeterrmine/main.nf
+++ b/tests/modules/sexdeterrmine/main.nf
@@ -9,7 +9,7 @@ workflow test_sexdeterrmine {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test3.single_end.markduplicates.sorted.bam'], checkIfExists: true) ]
+        file(params.test_data['homo_sapiens']['illumina']['test3_single_end_markduplicates_sorted_bam'], checkIfExists: true) ]
 
     SAMTOOLS_DEPTH ( input )
     SEXDETERRMINE ( SAMTOOLS_DEPTH.out.tsv, [] )
diff --git a/tests/modules/sexdeterrmine/test.yml b/tests/modules/sexdeterrmine/test.yml
index 54c471ba..bb3f701e 100644
--- a/tests/modules/sexdeterrmine/test.yml
+++ b/tests/modules/sexdeterrmine/test.yml
@@ -4,12 +4,12 @@
     - sexdeterrmine
   files:
     - path: output/samtools/test.tsv
-      md5sum: c894abd0c78ea7760e0b54bbafb93722
+      md5sum: fa2992ca1ea93a6e1b3e838476191935
     - path: output/samtools/versions.yml
       md5sum: dbd04b700335c8ad236bd667254c8dd8
     - path: output/sexdeterrmine/sexdeterrmine.json
-      md5sum: 16d9e7891d4c92bc1d66db2e70e9d86f
+      md5sum: bafb2419bb8630eda29a251c20e97166
     - path: output/sexdeterrmine/test_sexdet.tsv
-      md5sum: 7ffc35e478de66939819a9ca4a5df2d7
+      md5sum: 1cf8a2b97b38353eb97a96ab872dcca9
     - path: output/sexdeterrmine/versions.yml
       md5sum: 077361101e8e7997aec3da8a01e59eee

From 96260ced83ba3ad25ad03f85e085c459c54a1373 Mon Sep 17 00:00:00 2001
From: Thiseas Christos Lamnidis <thisseass@gmail.com>
Date: Mon, 23 May 2022 17:15:57 +0200
Subject: [PATCH 05/21] Add test data to config

---
 tests/config/test_data.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 559c0d6f..61bd1e40 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -219,10 +219,11 @@ params {
                 test2_paired_end_umi_unsorted_bam              = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
                 test2_paired_end_umi_unsorted_tagged_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
 
-
                 mitochon_standin_recalibrated_sorted_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam"
                 mitochon_standin_recalibrated_sorted_bam_bai   = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/mitochon_standin.recalibrated.sorted.bam.bai"
 
+                test3_single_end_markduplicates_sorted_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/test3.single_end.markduplicates.sorted.bam"
+
                 test_paired_end_sorted_cram                      = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
                 test_paired_end_sorted_cram_crai                 = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
                 test_paired_end_markduplicates_sorted_cram       = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"

From e36b79201df4f21e4657b08b4e85a2ca68c612f3 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 10 Jun 2022 10:52:13 +0200
Subject: [PATCH 06/21] Update Dockerfile

---
 modules/cellranger/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/cellranger/Dockerfile b/modules/cellranger/Dockerfile
index 3e52ca6a..266a24ef 100644
--- a/modules/cellranger/Dockerfile
+++ b/modules/cellranger/Dockerfile
@@ -1,4 +1,4 @@
-# Dockerfile to create container with Cell Ranger v6.1.2
+# Dockerfile to create container with Cell Ranger v7.0.0
 # Push to nfcore/cellranger:<VER>
 
 FROM continuumio/miniconda3:4.8.2

From 8032833e6e0fd3edeb20d4121885112249f273c4 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 10 Jun 2022 10:53:09 +0200
Subject: [PATCH 07/21] Update main.nf

---
 modules/cellranger/count/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/cellranger/count/main.nf b/modules/cellranger/count/main.nf
index 6a206b6e..7413c990 100644
--- a/modules/cellranger/count/main.nf
+++ b/modules/cellranger/count/main.nf
@@ -5,7 +5,7 @@ process CELLRANGER_COUNT {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
     }
-    container "nfcore/cellranger:6.1.2"
+    container "nfcore/cellranger:7.0.0"
 
     input:
     tuple val(meta), path(reads)

From e499abe572bc7c1322dfa66b767b0e65fe8c62ca Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 10 Jun 2022 10:53:48 +0200
Subject: [PATCH 08/21] Update main.nf

---
 modules/cellranger/mkgtf/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/cellranger/mkgtf/main.nf b/modules/cellranger/mkgtf/main.nf
index 9dc2fe1a..a115706d 100644
--- a/modules/cellranger/mkgtf/main.nf
+++ b/modules/cellranger/mkgtf/main.nf
@@ -5,7 +5,7 @@ process CELLRANGER_MKGTF {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
     }
-    container "nfcore/cellranger:6.1.2"
+    container "nfcore/cellranger:7.0.0"
 
     input:
     path gtf

From 61d87bb2bcbcd058e1af6e5f14bb821b8ae4ed3e Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 10 Jun 2022 10:54:06 +0200
Subject: [PATCH 09/21] Update main.nf

---
 modules/cellranger/mkref/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/cellranger/mkref/main.nf b/modules/cellranger/mkref/main.nf
index 11cf80e3..e1bfebde 100644
--- a/modules/cellranger/mkref/main.nf
+++ b/modules/cellranger/mkref/main.nf
@@ -5,7 +5,7 @@ process CELLRANGER_MKREF {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
     }
-    container "nfcore/cellranger:6.1.2"
+    container "nfcore/cellranger:7.0.0"
 
     input:
     path fasta

From cfcd93f3e78b1c7e7490b702be8a5fadb8a55d2d Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 10 Jun 2022 10:56:13 +0200
Subject: [PATCH 10/21] Update Dockerfile

---
 modules/cellranger/mkfastq/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/cellranger/mkfastq/Dockerfile b/modules/cellranger/mkfastq/Dockerfile
index 8660293a..7b6b84ec 100644
--- a/modules/cellranger/mkfastq/Dockerfile
+++ b/modules/cellranger/mkfastq/Dockerfile
@@ -1,4 +1,4 @@
-# Dockerfile to create container with Cell Ranger v6.1.2 and bcl2fastq v2.20.0
+# Dockerfile to create container with Cell Ranger v7.0.0 and bcl2fastq v2.20.0
 # Push to nfcore/cellrangermkfastq:<VER>
 
 FROM continuumio/miniconda3:4.8.2
@@ -17,7 +17,7 @@ RUN apt-get update --allow-releaseinfo-change \
 
 # Copy pre-downloaded bcl2fastq2 and cellranger file
 ENV BCL2FASTQ2_VER=v2-20-0-linux-x86-64 \
-    CELLRANGER_VER=6.1.2
+    CELLRANGER_VER=7.0.0
 COPY bcl2fastq2-$BCL2FASTQ2_VER.zip /tmp/bcl2fastq2-$BCL2FASTQ2_VER.zip
 COPY cellranger-$CELLRANGER_VER.tar.gz /opt/cellranger-$CELLRANGER_VER.tar.gz
 

From fe855a1c234b26540f0ef9eb10376619ae781ab3 Mon Sep 17 00:00:00 2001
From: "Thiseas C. Lamnidis" <thisseass@gmail.com>
Date: Fri, 10 Jun 2022 11:03:01 +0200
Subject: [PATCH 11/21] Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/sexdeterrmine/main.nf  |  4 ++--
 modules/sexdeterrmine/meta.yml | 10 +++++-----
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/sexdeterrmine/main.nf b/modules/sexdeterrmine/main.nf
index dd8b5a70..98c72307 100644
--- a/modules/sexdeterrmine/main.nf
+++ b/modules/sexdeterrmine/main.nf
@@ -9,7 +9,7 @@ process SEXDETERRMINE {
 
     input:
     tuple val(meta), path(depth)
-    path(sample_list_file)
+    path sample_list_file
 
     output:
     tuple val(meta), path("*.json"), emit: json
@@ -23,7 +23,7 @@ process SEXDETERRMINE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sample_list = sample_list_file ? '-f ${sample_list_file}' : ''
-    if ("$depth" == "${prefix}.tsv") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    if ("$depth" == "${prefix}.tsv") error "Input depth and output TSV names are the same, set prefix in module configuration to disambiguate!"
 
     """
     sexdeterrmine \\
diff --git a/modules/sexdeterrmine/meta.yml b/modules/sexdeterrmine/meta.yml
index 6e24c817..3f56b0ab 100644
--- a/modules/sexdeterrmine/meta.yml
+++ b/modules/sexdeterrmine/meta.yml
@@ -1,9 +1,10 @@
 name: "sexdeterrmine"
 description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
 keywords:
-  - "sex determination"
-  - "genetic sex"
-  - "relative coverage"
+  - sex determination
+  - genetic sex
+  - relative coverage
+  - ancient dna
 tools:
   - "sexdeterrmine":
       description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data."
@@ -19,10 +20,9 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  #
   - depth:
       type: file
-      description: output from samtools depth (with header)
+      description: Output from samtools depth (with header)
       pattern: "*"
 
 output:

From 62c4b59d100d36488323041ac1a9e88b392eba36 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <apeltzer@users.noreply.github.com>
Date: Fri, 10 Jun 2022 11:05:59 +0200
Subject: [PATCH 12/21] Update main.nf

---
 modules/cellranger/mkfastq/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/cellranger/mkfastq/main.nf b/modules/cellranger/mkfastq/main.nf
index 9c023bca..30c638ea 100644
--- a/modules/cellranger/mkfastq/main.nf
+++ b/modules/cellranger/mkfastq/main.nf
@@ -5,7 +5,7 @@ process CELLRANGER_MKFASTQ {
     if (params.enable_conda) {
         exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
     }
-    container "nfcore/cellrangermkfastq:6.1.2"
+    container "nfcore/cellrangermkfastq:7.0.0"
 
     input:
     path bcl

From 570a43ba4c2b3b632662ded334002bd528365382 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
Date: Fri, 10 Jun 2022 11:21:03 +0200
Subject: [PATCH 13/21] Fix tests

---
 tests/modules/cellranger/count/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/cellranger/count/test.yml b/tests/modules/cellranger/count/test.yml
index 121d9eea..e29baaf0 100644
--- a/tests/modules/cellranger/count/test.yml
+++ b/tests/modules/cellranger/count/test.yml
@@ -8,12 +8,12 @@
     - path: output/cellranger/sample-123/outs/metrics_summary.csv
       md5sum: 707df0f101d479d93f412ca74f9c4131
     - path: output/cellranger/sample-123/outs/molecule_info.h5
-      md5sum: 0e56836ef0725f2ab05f56ca5a71e55b
+      md5sum: a13bd7425f441c8d0eac8ffc50082996
     - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam
       md5sum: 15441da9cfceea0bb48c8b66b1b860df
     - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
       md5sum: 7c3d49c77016a09535aff61a027f750c
     - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
     - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
-      md5sum: cdad1cd7b215d7137cf92515e81a8525
+      md5sum: a5290f3e300a4070f3d68a0c2e215f54
     - path: output/cellranger/sample-123/outs/web_summary.html

From 4928dfad345f7b2a3a045140b95ea5a9f0a99e9e Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
Date: Fri, 10 Jun 2022 11:22:45 +0200
Subject: [PATCH 14/21] Trying to fix tests

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

diff --git a/tests/modules/cellranger/mkref/test.yml b/tests/modules/cellranger/mkref/test.yml
index e40592bb..3f63b59c 100644
--- a/tests/modules/cellranger/mkref/test.yml
+++ b/tests/modules/cellranger/mkref/test.yml
@@ -11,7 +11,7 @@
     - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
       md5sum: 6d9b5f409bfea95022bc25b9590e194e
     - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
-      md5sum: 5d8d1669cd251433505f183e1c9ed6bc
+      md5sum: 6cc817f0923062e780e6573806840cea
     - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
       md5sum: 22102926fadf5890e905ca71b2da3f35
     - path: output/cellranger/homo_sapiens_chr22_reference/star/SA

From 0479544e02354bbb0e775fab7f012a1d52ff896c Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 10 Jun 2022 09:46:14 +0000
Subject: [PATCH 15/21] Allow Git commit SHA's as version numbers

---
 tests/test_versions_yml.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_versions_yml.py b/tests/test_versions_yml.py
index 5d0bb39e..60a083c4 100644
--- a/tests/test_versions_yml.py
+++ b/tests/test_versions_yml.py
@@ -16,9 +16,9 @@ def _get_workflow_names():
         # test_config = yaml.safe_load(f.read_text())
         test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
         for workflow in test_config:
-            # https://github.com/nf-core/modules/pull/1242 - added to cover tests 
+            # https://github.com/nf-core/modules/pull/1242 - added to cover tests
             # that expect an error and therefore will not generate a versions.yml
-            if 'exit_code' not in workflow: 
+            if 'exit_code' not in workflow:
                 yield workflow["name"]
 
 
@@ -56,5 +56,5 @@ def test_ensure_valid_version_yml(workflow_dir):
     assert len(software_versions), "There must be at least one version emitted."
     for tool, version in software_versions.items():
         assert re.match(
-            r"^\d+.*", str(version)
+            r"(^\d+.*|^[a-z0-9]{40}$)", str(version)
         ), f"Version number for {tool} must start with a number. "

From 1fbe69cfcc13ab98ee20c7eb6fdb3aaac420a9d0 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
Date: Fri, 10 Jun 2022 11:46:23 +0200
Subject: [PATCH 16/21] Updated and fixed tests

---
 tests/modules/cellranger/count/test.yml | 54 +++++++++++++++++++++++--
 tests/modules/cellranger/mkgtf/test.yml |  4 +-
 tests/modules/cellranger/mkref/test.yml |  4 +-
 3 files changed, 55 insertions(+), 7 deletions(-)

diff --git a/tests/modules/cellranger/count/test.yml b/tests/modules/cellranger/count/test.yml
index e29baaf0..2f49daf5 100644
--- a/tests/modules/cellranger/count/test.yml
+++ b/tests/modules/cellranger/count/test.yml
@@ -1,10 +1,53 @@
 - name: cellranger count test_cellranger_count
-  command: nextflow run tests/modules/cellranger/count -entry test_cellranger_count -c tests/config/nextflow.config -c tests/modules/cellranger/count/nextflow.config
+  command: nextflow run ./tests/modules/cellranger/count -entry test_cellranger_count -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/count/nextflow.config
   tags:
-    - cellranger
     - cellranger/count
+    - cellranger
   files:
+    - path: output/cellranger/genome.filtered.gtf
+      md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
+    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
+      md5sum: f315020d899597c1b57e5fe9f60f4c3e
+    - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa.fai
+      md5sum: 3520cd30e1b100e55f578db9c855f685
+    - path: output/cellranger/homo_sapiens_chr22_reference/genes/genes.gtf.gz
+      md5sum: d1e05cd46684fa26d852b6bc9f05e31f
+    - path: output/cellranger/homo_sapiens_chr22_reference/reference.json
+      md5sum: 8405fd7f527a944eafb9c2909045840b
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/Genome
+      md5sum: 897cec2d191945335f8b320438bd9135
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/SA
+      md5sum: 7961129ac5d0e1706105be1d31c6b30c
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/SAindex
+      md5sum: dcceb480b30cda93fb8c63ddc339093b
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrLength.txt
+      md5sum: c81f40f27e72606d7d07097c1d56a5b5
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrName.txt
+      md5sum: 5ae68a67b70976ee95342a7451cb5af1
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrNameLength.txt
+      md5sum: b190587cae0531f3cf25552d8aa674db
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/chrStart.txt
+      md5sum: bc73df776dd3d5bb9cfcbcba60880519
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonGeTrInfo.tab
+      md5sum: 9129691eeb4ed0d02b17be879fa3edb0
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/exonInfo.tab
+      md5sum: 209b82f0683efd03e17d2c729676554f
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/geneInfo.tab
+      md5sum: 02a8f4575bdfcd4a42b4d8d07f2e9369
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/genomeParameters.txt
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
+      md5sum: 1082ab459363b3f2f7aabcef0979c1ed
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
+      md5sum: cedcb5f4e7d97bc548cd5daa022e092c
     - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5
+      md5sum: f8b6b7cc8248151a98c46d4ebec450c6
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/barcodes.tsv.gz
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/features.tsv.gz
+    - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix/matrix.mtx.gz
     - path: output/cellranger/sample-123/outs/metrics_summary.csv
       md5sum: 707df0f101d479d93f412ca74f9c4131
     - path: output/cellranger/sample-123/outs/molecule_info.h5
@@ -13,7 +56,12 @@
       md5sum: 15441da9cfceea0bb48c8b66b1b860df
     - path: output/cellranger/sample-123/outs/possorted_genome_bam.bam.bai
       md5sum: 7c3d49c77016a09535aff61a027f750c
-    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix
     - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix.h5
       md5sum: a5290f3e300a4070f3d68a0c2e215f54
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/barcodes.tsv.gz
+      md5sum: 5cc39ef0c7ac85f2b758b164aabf9157
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/features.tsv.gz
+      md5sum: 07d497c7ce3e22f374af7b2cf9b97d72
+    - path: output/cellranger/sample-123/outs/raw_feature_bc_matrix/matrix.mtx.gz
+      md5sum: bdce94a51f16e22d40301724080b76ee
     - path: output/cellranger/sample-123/outs/web_summary.html
diff --git a/tests/modules/cellranger/mkgtf/test.yml b/tests/modules/cellranger/mkgtf/test.yml
index 2130afd2..59eb9072 100644
--- a/tests/modules/cellranger/mkgtf/test.yml
+++ b/tests/modules/cellranger/mkgtf/test.yml
@@ -1,8 +1,8 @@
 - name: cellranger mkgtf test_cellranger_mkgtf
-  command: nextflow run tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c tests/config/nextflow.config -c tests/modules/cellranger/mkgtf/nextflow.config
+  command: nextflow run ./tests/modules/cellranger/mkgtf -entry test_cellranger_mkgtf -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/mkgtf/nextflow.config
   tags:
-    - cellranger
     - cellranger/mkgtf
+    - cellranger
   files:
     - path: output/cellranger/genome.filtered.gtf
       md5sum: a8b8a7b5039e05d3a9cf9151ea138b5b
diff --git a/tests/modules/cellranger/mkref/test.yml b/tests/modules/cellranger/mkref/test.yml
index 3f63b59c..83ec5f95 100644
--- a/tests/modules/cellranger/mkref/test.yml
+++ b/tests/modules/cellranger/mkref/test.yml
@@ -1,8 +1,8 @@
 - name: cellranger mkref test_cellranger_mkref
-  command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config -c ./tests/modules/cellranger/mkref/nextflow.config
+  command: nextflow run ./tests/modules/cellranger/mkref -entry test_cellranger_mkref -c ./tests/config/nextflow.config  -c ./tests/modules/cellranger/mkref/nextflow.config
   tags:
-    - cellranger
     - cellranger/mkref
+    - cellranger
   files:
     - path: output/cellranger/homo_sapiens_chr22_reference/fasta/genome.fa
       md5sum: f315020d899597c1b57e5fe9f60f4c3e

From 63f47551a84741e7f495e8b381788ae13efb3ec6 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
Date: Fri, 10 Jun 2022 11:52:30 +0200
Subject: [PATCH 17/21] Fix empty test having md5sum

---
 tests/modules/cellranger/count/test.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/modules/cellranger/count/test.yml b/tests/modules/cellranger/count/test.yml
index 2f49daf5..93e52c4a 100644
--- a/tests/modules/cellranger/count/test.yml
+++ b/tests/modules/cellranger/count/test.yml
@@ -38,9 +38,7 @@
     - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbInfo.txt
       md5sum: 1082ab459363b3f2f7aabcef0979c1ed
     - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.fromGTF.out.tab
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cellranger/homo_sapiens_chr22_reference/star/sjdbList.out.tab
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cellranger/homo_sapiens_chr22_reference/star/transcriptInfo.tab
       md5sum: cedcb5f4e7d97bc548cd5daa022e092c
     - path: output/cellranger/sample-123/outs/filtered_feature_bc_matrix.h5

From a0747b1405d817261a3738fc4c11c3dd61103257 Mon Sep 17 00:00:00 2001
From: Alexander Peltzer <alexander.peltzer@boehringer-ingelheim.com>
Date: Fri, 10 Jun 2022 11:53:28 +0200
Subject: [PATCH 18/21] Remove empty file md5sum

---
 tests/modules/cellranger/mkfastq/test.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/tests/modules/cellranger/mkfastq/test.yml b/tests/modules/cellranger/mkfastq/test.yml
index 890f2557..273d8fca 100644
--- a/tests/modules/cellranger/mkfastq/test.yml
+++ b/tests/modules/cellranger/mkfastq/test.yml
@@ -5,7 +5,6 @@
     - cellranger/mkfastq
   files:
     - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
 - name: cellranger mkfastq test_cellranger_mkfastq_illumina
   command: nextflow run tests/modules/cellranger/mkfastq -entry test_cellranger_mkfastq_illumina -c tests/config/nextflow.config -c ./tests/modules/cellranger/mkfastq/nextflow.config -stub-run
   tags:
@@ -13,4 +12,3 @@
     - cellranger/mkfastq
   files:
     - path: output/cellranger/cellranger-tiny-bcl-1/outs/fastq_path/fake_file.fastq.gz
-      md5sum: d41d8cd98f00b204e9800998ecf8427e

From 6a1cbce0f538466fd3152a17217f71289417d91c Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 10 Jun 2022 12:54:08 +0200
Subject: [PATCH 19/21] Update tests/test_versions_yml.py

Co-authored-by: Fabian Egli <fabianegli@users.noreply.github.com>
---
 tests/test_versions_yml.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_versions_yml.py b/tests/test_versions_yml.py
index 60a083c4..a5ebb08d 100644
--- a/tests/test_versions_yml.py
+++ b/tests/test_versions_yml.py
@@ -56,5 +56,5 @@ def test_ensure_valid_version_yml(workflow_dir):
     assert len(software_versions), "There must be at least one version emitted."
     for tool, version in software_versions.items():
         assert re.match(
-            r"(^\d+.*|^[a-z0-9]{40}$)", str(version)
+            r"(^\d+.*|^[a-f0-9]{40}$)", str(version)
         ), f"Version number for {tool} must start with a number. "

From 25c742dc69daaa41cf1b49fed4955e92b1cb9bbd Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 10 Jun 2022 10:56:56 +0000
Subject: [PATCH 20/21] Commit suggestions from code review

---
 tests/test_versions_yml.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/test_versions_yml.py b/tests/test_versions_yml.py
index a5ebb08d..bcff7b01 100644
--- a/tests/test_versions_yml.py
+++ b/tests/test_versions_yml.py
@@ -56,5 +56,5 @@ def test_ensure_valid_version_yml(workflow_dir):
     assert len(software_versions), "There must be at least one version emitted."
     for tool, version in software_versions.items():
         assert re.match(
-            r"(^\d+.*|^[a-f0-9]{40}$)", str(version)
-        ), f"Version number for {tool} must start with a number. "
+            r"^\d.*|^[a-f0-9]{40}$", str(version)
+        ), f"Version number for {tool} must start with a number, or be a Git SHA. "

From f8bd7902d9e1563f14fcf296e1ede712599d13f3 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Fri, 10 Jun 2022 11:01:40 +0000
Subject: [PATCH 21/21] Update Git SHA messagre

---
 tests/test_versions_yml.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_versions_yml.py b/tests/test_versions_yml.py
index bcff7b01..7da6707d 100644
--- a/tests/test_versions_yml.py
+++ b/tests/test_versions_yml.py
@@ -57,4 +57,4 @@ def test_ensure_valid_version_yml(workflow_dir):
     for tool, version in software_versions.items():
         assert re.match(
             r"^\d.*|^[a-f0-9]{40}$", str(version)
-        ), f"Version number for {tool} must start with a number, or be a Git SHA. "
+        ), f"Version number for {tool} must start with a number, or be a Git SHA commit id. "