From d2004a2b769d9ff6c2f8fd8a1e1d0e5660fcc3f9 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Sun, 1 May 2022 21:14:01 +0200
Subject: [PATCH 01/11] update cnvpytor

---
 modules/cnvpytor/callcnvs/main.nf        | 6 +++---
 modules/cnvpytor/histogram/main.nf       | 6 +++---
 modules/cnvpytor/importreaddepth/main.nf | 6 +++---
 modules/cnvpytor/partition/main.nf       | 6 +++---
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/modules/cnvpytor/callcnvs/main.nf b/modules/cnvpytor/callcnvs/main.nf
index 17675cde..fcb36ba5 100644
--- a/modules/cnvpytor/callcnvs/main.nf
+++ b/modules/cnvpytor/callcnvs/main.nf
@@ -2,10 +2,10 @@ process CNVPYTOR_CALLCNVS {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
-        'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
+        'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(pytor)
diff --git a/modules/cnvpytor/histogram/main.nf b/modules/cnvpytor/histogram/main.nf
index 9e59c6b8..f6e9dd25 100644
--- a/modules/cnvpytor/histogram/main.nf
+++ b/modules/cnvpytor/histogram/main.nf
@@ -2,10 +2,10 @@ process CNVPYTOR_HISTOGRAM {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
-        'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
+        'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(pytor)
diff --git a/modules/cnvpytor/importreaddepth/main.nf b/modules/cnvpytor/importreaddepth/main.nf
index 162da719..059c19a5 100644
--- a/modules/cnvpytor/importreaddepth/main.nf
+++ b/modules/cnvpytor/importreaddepth/main.nf
@@ -2,10 +2,10 @@ process CNVPYTOR_IMPORTREADDEPTH {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
-        'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
+        'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input_file), path(index)
diff --git a/modules/cnvpytor/partition/main.nf b/modules/cnvpytor/partition/main.nf
index 0311bdfc..8365cb29 100644
--- a/modules/cnvpytor/partition/main.nf
+++ b/modules/cnvpytor/partition/main.nf
@@ -2,10 +2,10 @@ process CNVPYTOR_PARTITION {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
-        'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
+        'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(pytor)

From 9a9f3e97dedd3cf72720cca5588df4d4edd35d71 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Sun, 1 May 2022 21:51:40 +0200
Subject: [PATCH 02/11] fix md5sums

---
 tests/modules/cnvpytor/callcnvs/test.yml        | 3 ---
 tests/modules/cnvpytor/histogram/test.yml       | 3 ---
 tests/modules/cnvpytor/importreaddepth/test.yml | 4 ----
 tests/modules/cnvpytor/partition/test.yml       | 3 ---
 4 files changed, 13 deletions(-)

diff --git a/tests/modules/cnvpytor/callcnvs/test.yml b/tests/modules/cnvpytor/callcnvs/test.yml
index 4565151e..e284ab53 100644
--- a/tests/modules/cnvpytor/callcnvs/test.yml
+++ b/tests/modules/cnvpytor/callcnvs/test.yml
@@ -5,9 +5,7 @@
     - cnvpytor/callcnvs
   files:
     - path: output/cnvpytor/test.tsv
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: output/cnvpytor/versions.yml
-      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
@@ -17,4 +15,3 @@
   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 0543fcc3..f67901d4 100644
--- a/tests/modules/cnvpytor/histogram/test.yml
+++ b/tests/modules/cnvpytor/histogram/test.yml
@@ -5,9 +5,7 @@
     - cnvpytor/histogram
   files:
     - path: output/cnvpytor/test.pytor
-      md5sum: aa03a8fa15b39f77816705a48e10312a
     - path: output/cnvpytor/versions.yml
-      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
@@ -17,4 +15,3 @@
   files:
     - path: output/cnvpytor/test.pytor
     - path: output/cnvpytor/versions.yml
-      md5sum: 0f4d75c4f3a3eb26c22616d12b0b78b2
diff --git a/tests/modules/cnvpytor/importreaddepth/test.yml b/tests/modules/cnvpytor/importreaddepth/test.yml
index b148c38e..a2530c26 100644
--- a/tests/modules/cnvpytor/importreaddepth/test.yml
+++ b/tests/modules/cnvpytor/importreaddepth/test.yml
@@ -6,7 +6,6 @@
   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
@@ -16,7 +15,6 @@
   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
@@ -26,7 +24,6 @@
   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
@@ -36,4 +33,3 @@
   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 10232097..e24a1200 100644
--- a/tests/modules/cnvpytor/partition/test.yml
+++ b/tests/modules/cnvpytor/partition/test.yml
@@ -5,9 +5,7 @@
     - cnvpytor/partition
   files:
     - path: output/cnvpytor/test.pytor
-      md5sum: aa03a8fa15b39f77816705a48e10312a
     - path: output/cnvpytor/versions.yml
-      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
@@ -17,4 +15,3 @@
   files:
     - path: output/cnvpytor/test.pytor
     - path: output/cnvpytor/versions.yml
-      md5sum: 7fd6ec952a316463bcd324f176b46b64

From 2990dc8357dcf3bb53aef8cf5a7c9e8c8f5caa9b Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:20:05 +0200
Subject: [PATCH 03/11] callcnv module

---
 modules/cnvpytor/callcnvs/main.nf  | 14 +++++++-------
 modules/cnvpytor/callcnvs/meta.yml | 11 +++++++----
 2 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/modules/cnvpytor/callcnvs/main.nf b/modules/cnvpytor/callcnvs/main.nf
index fcb36ba5..c3866095 100644
--- a/modules/cnvpytor/callcnvs/main.nf
+++ b/modules/cnvpytor/callcnvs/main.nf
@@ -9,10 +9,11 @@ process CNVPYTOR_CALLCNVS {
 
     input:
     tuple val(meta), path(pytor)
+    val bin_sizes
 
     output:
-    tuple val(meta), path("*.tsv"), emit: cnvs
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("${pytor.baseName}.pytor")	, emit: pytor
+    path "versions.yml"                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,22 +24,21 @@ process CNVPYTOR_CALLCNVS {
     """
     cnvpytor \\
         -root $pytor \\
-        -call $args > ${prefix}.tsv
+        -call $bin_sizes
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.tsv
+    touch ${pytor.baseName}.pytor
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 }
diff --git a/modules/cnvpytor/callcnvs/meta.yml b/modules/cnvpytor/callcnvs/meta.yml
index edfc462a..6ba46b6f 100644
--- a/modules/cnvpytor/callcnvs/meta.yml
+++ b/modules/cnvpytor/callcnvs/meta.yml
@@ -17,8 +17,11 @@ input:
         e.g. [ id:'test']
   - pytor:
       type: file
-      description: cnvpytor root file
+      description: pytor file containing partitions of read depth histograms using mean-shift method
       pattern: "*.{pytor}"
+  - bin_sizes:
+      type: string
+      description: list of binsizes separated by space e.g. "1000 10000" and "1000"
 
 output:
   - meta:
@@ -26,10 +29,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - cnvs:
+  - pytor:
       type: file
-      description: file containing identified copy numer variations
-      pattern: "*.{tsv}"
+      description: pytor files containing cnv calls
+      pattern: "*.{pytor}"
   - versions:
       type: file
       description: File containing software versions

From 07e026054a018139da73534acacfdcaf8762173e Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:24:54 +0200
Subject: [PATCH 04/11] histogram

---
 modules/cnvpytor/histogram/main.nf  | 8 +++++---
 modules/cnvpytor/histogram/meta.yml | 3 +++
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/modules/cnvpytor/histogram/main.nf b/modules/cnvpytor/histogram/main.nf
index f6e9dd25..1906fa36 100644
--- a/modules/cnvpytor/histogram/main.nf
+++ b/modules/cnvpytor/histogram/main.nf
@@ -9,6 +9,8 @@ process CNVPYTOR_HISTOGRAM {
 
     input:
     tuple val(meta), path(pytor)
+    val bin_sizes
+
 
     output:
     tuple val(meta), path("${pytor.baseName}.pytor")	, emit: pytor
@@ -18,15 +20,15 @@ process CNVPYTOR_HISTOGRAM {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: '1000'
+    def bins = bin_sizes ?: '1000'
     """
     cnvpytor \\
         -root $pytor \\
-        -his $args
+        -his $bins
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 
diff --git a/modules/cnvpytor/histogram/meta.yml b/modules/cnvpytor/histogram/meta.yml
index fcad2221..4855f26d 100644
--- a/modules/cnvpytor/histogram/meta.yml
+++ b/modules/cnvpytor/histogram/meta.yml
@@ -22,6 +22,9 @@ input:
       type: file
       description: pytor file containing read depth data
       pattern: "*.{pytor}"
+  - bin_sizes:
+      type: string
+      description: list of binsizes separated by space e.g. "1000 10000" and "1000"
 
 output:
   - meta:

From 7cc47f6ba6a3aba385fde62bb8c2e0a7ae435ed3 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:25:20 +0200
Subject: [PATCH 05/11] importrd

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

diff --git a/modules/cnvpytor/importreaddepth/main.nf b/modules/cnvpytor/importreaddepth/main.nf
index 059c19a5..ff00c0b0 100644
--- a/modules/cnvpytor/importreaddepth/main.nf
+++ b/modules/cnvpytor/importreaddepth/main.nf
@@ -43,7 +43,7 @@ process CNVPYTOR_IMPORTREADDEPTH {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 }

From 829c15c98b1447f9445690e29f2b684dbe053f65 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:26:34 +0200
Subject: [PATCH 06/11] partition

---
 modules/cnvpytor/partition/main.nf  | 7 ++++---
 modules/cnvpytor/partition/meta.yml | 3 +++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/modules/cnvpytor/partition/main.nf b/modules/cnvpytor/partition/main.nf
index 8365cb29..42a5ec78 100644
--- a/modules/cnvpytor/partition/main.nf
+++ b/modules/cnvpytor/partition/main.nf
@@ -9,6 +9,7 @@ process CNVPYTOR_PARTITION {
 
     input:
     tuple val(meta), path(pytor)
+    val bin_sizes
 
     output:
     tuple val(meta), path("${pytor.baseName}.pytor"), emit: pytor
@@ -18,15 +19,15 @@ process CNVPYTOR_PARTITION {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def bins = bin_sizes ?: '1000'
     """
     cnvpytor \\
         -root $pytor \\
-        -partition $args
+        -partition $bins
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 
diff --git a/modules/cnvpytor/partition/meta.yml b/modules/cnvpytor/partition/meta.yml
index a72cea4c..bb7a047e 100644
--- a/modules/cnvpytor/partition/meta.yml
+++ b/modules/cnvpytor/partition/meta.yml
@@ -22,6 +22,9 @@ input:
       type: file
       description: pytor file containing read depth data
       pattern: "*.{pytor}"
+  - bin_sizes:
+      type: string
+      description: list of binsizes separated by space e.g. "1000 10000" and "1000"
 
 output:
   - meta:

From 3efa931bf6a77a6f6942ebfe4ba8620119f49327 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:26:46 +0200
Subject: [PATCH 07/11] view

---
 modules/cnvpytor/view/main.nf  | 59 ++++++++++++++++++++++++++++++++++
 modules/cnvpytor/view/meta.yml | 44 +++++++++++++++++++++++++
 2 files changed, 103 insertions(+)
 create mode 100644 modules/cnvpytor/view/main.nf
 create mode 100644 modules/cnvpytor/view/meta.yml

diff --git a/modules/cnvpytor/view/main.nf b/modules/cnvpytor/view/main.nf
new file mode 100644
index 00000000..c4e49a78
--- /dev/null
+++ b/modules/cnvpytor/view/main.nf
@@ -0,0 +1,59 @@
+process CNVPYTOR_VIEW {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::cnvpytor=1.2.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/cnvpytor:1.2.1--pyhdfd78af_0':
+        'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(pytor)
+    val bin_sizes
+    val output_format
+
+    output:
+    tuple val(meta), path("*.vcf"), emit: vcf      , optional: true
+    tuple val(meta), path("*.tsv"), emit: tsv      , optional: true
+    tuple val(meta), path("*.xls"), emit: xls      , optional: true
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def output_suffix = output_format ?: 'vcf'
+    """
+
+    python3 <<CODE
+    import cnvpytor,os
+    from pathlib import Path
+    pytor_files = Path.cwd().glob("*.pytor")
+    binsizes = "${bin_sizes}".split(" ")
+    for pytor_file in pytor_files:
+        for binsize in binsizes:
+            file_list = [str(pytor_file)]
+            app = cnvpytor.Viewer(file_list, params={} )
+            outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}")
+            app.print_filename = outputfile
+            app.bin_size = int(binsize)
+            app.print_calls_file()
+    CODE
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def output_suffix = output_format ?: 'vcf'
+    """
+    touch ${pytor.baseName}.${output_suffix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/cnvpytor/view/meta.yml b/modules/cnvpytor/view/meta.yml
new file mode 100644
index 00000000..d4456469
--- /dev/null
+++ b/modules/cnvpytor/view/meta.yml
@@ -0,0 +1,44 @@
+name: cnvpytor_view
+description: view function to generate vcfs
+keywords:
+  - cnv calling
+tools:
+  - cnvpytor:
+      description: calling CNVs using read depth
+      homepage: https://github.com/abyzovlab/CNVpytor
+      documentation: https://github.com/abyzovlab/CNVpytor
+      tool_dev_url: https://github.com/abyzovlab/CNVpytor
+      doi: "10.1101/2021.01.27.428472v1"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - pytor:
+      type: file
+      description: pytor file containing read depth data
+      pattern: "*.{pytor}"
+  - bin_sizes:
+      type: string
+      description: list of binsizes separated by space e.g. "1000 10000" and "1000"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - partitions:
+      type: file
+      description: pytor file containing partitions of read depth histograms using mean-shift method
+      pattern: "*.{pytor}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@sima-r"

From 46e5752b82fb9d0f8d472b3d87efa7419f658279 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:32:45 +0200
Subject: [PATCH 08/11] update tests

---
 tests/modules/cnvpytor/callcnvs/test.yml    |  4 +-
 tests/modules/cnvpytor/view/main.nf         | 43 +++++++++++++++++++++
 tests/modules/cnvpytor/view/nextflow.config |  7 ++++
 tests/modules/cnvpytor/view/test.yml        | 26 +++++++++++++
 4 files changed, 78 insertions(+), 2 deletions(-)
 create mode 100644 tests/modules/cnvpytor/view/main.nf
 create mode 100644 tests/modules/cnvpytor/view/nextflow.config
 create mode 100644 tests/modules/cnvpytor/view/test.yml

diff --git a/tests/modules/cnvpytor/callcnvs/test.yml b/tests/modules/cnvpytor/callcnvs/test.yml
index e284ab53..fd07db4c 100644
--- a/tests/modules/cnvpytor/callcnvs/test.yml
+++ b/tests/modules/cnvpytor/callcnvs/test.yml
@@ -4,7 +4,7 @@
     - cnvpytor
     - cnvpytor/callcnvs
   files:
-    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/test.pytor
     - path: output/cnvpytor/versions.yml
 
 - name: cnvpytor callcnvs test_cnvpytor_callcnvs stub
@@ -13,5 +13,5 @@
     - cnvpytor
     - cnvpytor/callcnvs
   files:
-    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/test.pytor
     - path: output/cnvpytor/versions.yml
diff --git a/tests/modules/cnvpytor/view/main.nf b/tests/modules/cnvpytor/view/main.nf
new file mode 100644
index 00000000..30177c44
--- /dev/null
+++ b/tests/modules/cnvpytor/view/main.nf
@@ -0,0 +1,43 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { CNVPYTOR_VIEW } from '../../../../modules/cnvpytor/view/main.nf'
+
+workflow test_cnvpytor_view {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    bin_sizes = "10000 100000"
+
+    CNVPYTOR_VIEW ( input, bin_sizes, [] )
+}
+
+workflow test_cnvpytor_view_tsvout {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    bin_sizes = "10000"
+    output_suffix = "tsv"
+
+    CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
+}
+
+workflow test_cnvpytor_view_stub {
+
+    input = [
+        [ id:'test'], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+    ]
+
+    bin_sizes = "10000"
+    output_suffix = "tsv"
+
+    CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
+}
diff --git a/tests/modules/cnvpytor/view/nextflow.config b/tests/modules/cnvpytor/view/nextflow.config
new file mode 100644
index 00000000..6d2cc1fb
--- /dev/null
+++ b/tests/modules/cnvpytor/view/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: CNVPYTOR_VIEW {
+        ext.args = '10000 100000'
+    }
+}
diff --git a/tests/modules/cnvpytor/view/test.yml b/tests/modules/cnvpytor/view/test.yml
new file mode 100644
index 00000000..38f75003
--- /dev/null
+++ b/tests/modules/cnvpytor/view/test.yml
@@ -0,0 +1,26 @@
+- name: cnvpytor view test_cnvpytor_view
+  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test_10000.vcf
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor view test_cnvpytor_view tsv
+  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view_tsvout -c tests/config/nextflow.config
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/versions.yml
+
+- name: cnvpytor view test_cnvpytor_view stub
+  command: nextflow run tests/modules/cnvpytor/view -entry test_cnvpytor_view_stub -c tests/config/nextflow.config  -stub-run
+  tags:
+    - cnvpytor
+    - cnvpytor/view
+  files:
+    - path: output/cnvpytor/test.vcf
+    - path: output/cnvpytor/versions.yml

From 19cfb4e95196d0e8cc14a67ecb8f1ed0b0fcc3a7 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 14:53:56 +0200
Subject: [PATCH 09/11] update meta files

---
 modules/cnvpytor/histogram/main.nf        |  2 +-
 modules/cnvpytor/histogram/meta.yml       |  1 +
 modules/cnvpytor/importreaddepth/main.nf  |  2 +-
 modules/cnvpytor/importreaddepth/meta.yml |  1 +
 modules/cnvpytor/partition/main.nf        |  2 +-
 modules/cnvpytor/partition/meta.yml       |  1 +
 modules/cnvpytor/view/main.nf             |  3 ++-
 modules/cnvpytor/view/meta.yml            | 15 ++++++++++++---
 tests/modules/cnvpytor/view/main.nf       |  7 +++----
 tests/modules/cnvpytor/view/test.yml      |  2 +-
 10 files changed, 24 insertions(+), 12 deletions(-)

diff --git a/modules/cnvpytor/histogram/main.nf b/modules/cnvpytor/histogram/main.nf
index 1906fa36..fd2ebe14 100644
--- a/modules/cnvpytor/histogram/main.nf
+++ b/modules/cnvpytor/histogram/main.nf
@@ -38,7 +38,7 @@ process CNVPYTOR_HISTOGRAM {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 }
diff --git a/modules/cnvpytor/histogram/meta.yml b/modules/cnvpytor/histogram/meta.yml
index 4855f26d..ecd48b9a 100644
--- a/modules/cnvpytor/histogram/meta.yml
+++ b/modules/cnvpytor/histogram/meta.yml
@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@sima-r"
+  - "@ramprasadn"
diff --git a/modules/cnvpytor/importreaddepth/main.nf b/modules/cnvpytor/importreaddepth/main.nf
index ff00c0b0..6f9abae9 100644
--- a/modules/cnvpytor/importreaddepth/main.nf
+++ b/modules/cnvpytor/importreaddepth/main.nf
@@ -32,7 +32,7 @@ process CNVPYTOR_IMPORTREADDEPTH {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 
diff --git a/modules/cnvpytor/importreaddepth/meta.yml b/modules/cnvpytor/importreaddepth/meta.yml
index 1cf3c0d0..8b58887e 100644
--- a/modules/cnvpytor/importreaddepth/meta.yml
+++ b/modules/cnvpytor/importreaddepth/meta.yml
@@ -52,3 +52,4 @@ output:
 
 authors:
   - "@sima-r"
+  - "@ramprasadn"
diff --git a/modules/cnvpytor/partition/main.nf b/modules/cnvpytor/partition/main.nf
index 42a5ec78..6d7a9c6b 100644
--- a/modules/cnvpytor/partition/main.nf
+++ b/modules/cnvpytor/partition/main.nf
@@ -37,7 +37,7 @@ process CNVPYTOR_PARTITION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 }
diff --git a/modules/cnvpytor/partition/meta.yml b/modules/cnvpytor/partition/meta.yml
index bb7a047e..17b5e199 100644
--- a/modules/cnvpytor/partition/meta.yml
+++ b/modules/cnvpytor/partition/meta.yml
@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@sima-r"
+  - "@ramprasadn"
diff --git a/modules/cnvpytor/view/main.nf b/modules/cnvpytor/view/main.nf
index c4e49a78..72726615 100644
--- a/modules/cnvpytor/view/main.nf
+++ b/modules/cnvpytor/view/main.nf
@@ -23,13 +23,14 @@ process CNVPYTOR_VIEW {
 
     script:
     def output_suffix = output_format ?: 'vcf'
+    def bins = bin_sizes ?: '1000'
     """
 
     python3 <<CODE
     import cnvpytor,os
     from pathlib import Path
     pytor_files = Path.cwd().glob("*.pytor")
-    binsizes = "${bin_sizes}".split(" ")
+    binsizes = "${bins}".split(" ")
     for pytor_file in pytor_files:
         for binsize in binsizes:
             file_list = [str(pytor_file)]
diff --git a/modules/cnvpytor/view/meta.yml b/modules/cnvpytor/view/meta.yml
index d4456469..0f9bbb43 100644
--- a/modules/cnvpytor/view/meta.yml
+++ b/modules/cnvpytor/view/meta.yml
@@ -31,10 +31,18 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - partitions:
+  - tsv:
       type: file
-      description: pytor file containing partitions of read depth histograms using mean-shift method
-      pattern: "*.{pytor}"
+      description: tsv file containing cnv calls
+      pattern: "*.{tsv}"
+  - vcf:
+      type: file
+      description: vcf file containing cnv calls
+      pattern: "*.{vcf}"
+  - xls:
+      type: file
+      description: xls file containing cnv calls
+      pattern: "*.{xls}"
   - versions:
       type: file
       description: File containing software versions
@@ -42,3 +50,4 @@ output:
 
 authors:
   - "@sima-r"
+  - "@ramprasadn"
diff --git a/tests/modules/cnvpytor/view/main.nf b/tests/modules/cnvpytor/view/main.nf
index 30177c44..b865dd6d 100644
--- a/tests/modules/cnvpytor/view/main.nf
+++ b/tests/modules/cnvpytor/view/main.nf
@@ -23,10 +23,9 @@ workflow test_cnvpytor_view_tsvout {
         file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
     ]
 
-    bin_sizes = "10000"
     output_suffix = "tsv"
 
-    CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
+    CNVPYTOR_VIEW ( input, [], output_suffix )
 }
 
 workflow test_cnvpytor_view_stub {
@@ -36,8 +35,8 @@ workflow test_cnvpytor_view_stub {
         file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
     ]
 
-    bin_sizes = "10000"
-    output_suffix = "tsv"
+    bin_sizes = []
+    output_suffix = []
 
     CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
 }
diff --git a/tests/modules/cnvpytor/view/test.yml b/tests/modules/cnvpytor/view/test.yml
index 38f75003..9c8b346b 100644
--- a/tests/modules/cnvpytor/view/test.yml
+++ b/tests/modules/cnvpytor/view/test.yml
@@ -13,7 +13,7 @@
     - cnvpytor
     - cnvpytor/view
   files:
-    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/test_1000.tsv
     - path: output/cnvpytor/versions.yml
 
 - name: cnvpytor view test_cnvpytor_view stub

From 26311aba2ace0eda4201651abe9276dbd8c2aef0 Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 3 May 2022 15:04:37 +0200
Subject: [PATCH 10/11] fix minor errors

---
 modules/cnvpytor/callcnvs/main.nf    | 2 +-
 modules/cnvpytor/view/meta.yml       | 3 +++
 tests/modules/cnvpytor/view/test.yml | 1 +
 3 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules/cnvpytor/callcnvs/main.nf b/modules/cnvpytor/callcnvs/main.nf
index c3866095..092f6def 100644
--- a/modules/cnvpytor/callcnvs/main.nf
+++ b/modules/cnvpytor/callcnvs/main.nf
@@ -19,7 +19,7 @@ process CNVPYTOR_CALLCNVS {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: '1000'
+    def bins = bin_sizes ?: '1000'
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     cnvpytor \\
diff --git a/modules/cnvpytor/view/meta.yml b/modules/cnvpytor/view/meta.yml
index 0f9bbb43..1392e90e 100644
--- a/modules/cnvpytor/view/meta.yml
+++ b/modules/cnvpytor/view/meta.yml
@@ -24,6 +24,9 @@ input:
   - bin_sizes:
       type: string
       description: list of binsizes separated by space e.g. "1000 10000" and "1000"
+  - output_format:
+      type: string
+      description: output format of the cnv calls. Valid entries are "tsv", "vcf", and "xls"
 
 output:
   - meta:
diff --git a/tests/modules/cnvpytor/view/test.yml b/tests/modules/cnvpytor/view/test.yml
index 9c8b346b..ea8ab792 100644
--- a/tests/modules/cnvpytor/view/test.yml
+++ b/tests/modules/cnvpytor/view/test.yml
@@ -5,6 +5,7 @@
     - cnvpytor/view
   files:
     - path: output/cnvpytor/test_10000.vcf
+    - path: output/cnvpytor/test_100000.vcf
     - path: output/cnvpytor/versions.yml
 
 - name: cnvpytor view test_cnvpytor_view tsv

From ea1f5daf449190dd3b8550c1307f14aa3371413d Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 5 May 2022 17:28:49 +0200
Subject: [PATCH 11/11] polish python script in view

---
 modules/cnvpytor/view/main.nf | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/modules/cnvpytor/view/main.nf b/modules/cnvpytor/view/main.nf
index 72726615..ad2249b8 100644
--- a/modules/cnvpytor/view/main.nf
+++ b/modules/cnvpytor/view/main.nf
@@ -29,16 +29,14 @@ process CNVPYTOR_VIEW {
     python3 <<CODE
     import cnvpytor,os
     from pathlib import Path
-    pytor_files = Path.cwd().glob("*.pytor")
+    pytor_file = Path("$pytor")
     binsizes = "${bins}".split(" ")
-    for pytor_file in pytor_files:
-        for binsize in binsizes:
-            file_list = [str(pytor_file)]
-            app = cnvpytor.Viewer(file_list, params={} )
-            outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}")
-            app.print_filename = outputfile
-            app.bin_size = int(binsize)
-            app.print_calls_file()
+    for binsize in binsizes:
+        app = cnvpytor.Viewer(["$pytor"], params={} )
+        outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}")
+        app.print_filename = outputfile
+        app.bin_size = int(binsize)
+        app.print_calls_file()
     CODE
 
     cat <<-END_VERSIONS > versions.yml