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 1/6] 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 2/6] 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 3/6] 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 4/6] 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 5/6] 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 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 6/6] 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: