From 9c708181e0c60fa9bc5ebd0e77fc5fd6033cdd92 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Tue, 3 Sep 2024 12:25:22 +0200
Subject: [PATCH 01/16] vcfpolyx, 1st commit

---
 .../nf-core/jvarkit/vcfpolyx/environment.yml  |  9 ++
 modules/nf-core/jvarkit/vcfpolyx/main.nf      | 89 +++++++++++++++++++
 modules/nf-core/jvarkit/vcfpolyx/meta.yml     | 45 ++++++++++
 .../jvarkit/vcfpolyx/tests/main.nf.test       | 68 ++++++++++++++
 .../nf-core/jvarkit/vcfpolyx/tests/tags.yml   |  2 +
 5 files changed, 213 insertions(+)
 create mode 100644 modules/nf-core/jvarkit/vcfpolyx/environment.yml
 create mode 100644 modules/nf-core/jvarkit/vcfpolyx/main.nf
 create mode 100644 modules/nf-core/jvarkit/vcfpolyx/meta.yml
 create mode 100644 modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
 create mode 100644 modules/nf-core/jvarkit/vcfpolyx/tests/tags.yml

diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
new file mode 100644
index 00000000000..980e48236e6
--- /dev/null
+++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "jvarkit_vcfpolyx"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::jvarkit=2024.08.25"
diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf
new file mode 100644
index 00000000000..5a220cf31b5
--- /dev/null
+++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf
@@ -0,0 +1,89 @@
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process JVARKIT_VCFPOLYX {
+    tag '$bam'
+    label 'process_single'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_0':
+        'biocontainers/jvarkit:2024.08.25--hdfd78af_0' }"
+
+    input:
+    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    path bam
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    path "*.bam", emit: bam
+    // TODO nf-core: List additional required output channels/values here
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    
+    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
+    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    """
+    samtools \\
+        sort \\
+        $args \\
+        -@ $task.cpus \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        jvarkit: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    
+    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
+    //               Have a look at the following examples:
+    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
+    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        jvarkit: \$(samtools --version |& sed '1!d ; s/samtools //')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
new file mode 100644
index 00000000000..a2b1b3ead7f
--- /dev/null
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -0,0 +1,45 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "jvarkit_vcfpolyx"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "jvarkit":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "Java utilities for Bioinformatics."
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "None"
+      doi: ""
+      licence: ['MIT License']
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  #
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  #
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  ## TODO nf-core: Delete / customise this example output
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@lindenb"
+maintainers:
+  - "@lindenb"
diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
new file mode 100644
index 00000000000..93952cba65d
--- /dev/null
+++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
@@ -0,0 +1,68 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test jvarkit/vcfpolyx
+nextflow_process {
+
+    name "Test Process JVARKIT_VCFPOLYX"
+    script "../main.nf"
+    process "JVARKIT_VCFPOLYX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "jvarkit"
+    tag "jvarkit/vcfpolyx"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                
+                input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                
+                input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/tags.yml b/modules/nf-core/jvarkit/vcfpolyx/tests/tags.yml
new file mode 100644
index 00000000000..475476a589b
--- /dev/null
+++ b/modules/nf-core/jvarkit/vcfpolyx/tests/tags.yml
@@ -0,0 +1,2 @@
+jvarkit/vcfpolyx:
+  - "modules/nf-core/jvarkit/vcfpolyx/**"

From a26daa1afadeb9818500a9c66f9c16c77a6abda2 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Tue, 3 Sep 2024 17:45:32 +0200
Subject: [PATCH 02/16] vcfpolyx

---
 modules/nf-core/jvarkit/vcfpolyx/main.nf      | 95 ++++++++-----------
 modules/nf-core/jvarkit/vcfpolyx/meta.yml     | 16 +++-
 .../jvarkit/vcfpolyx/tests/main.nf.test       | 45 ++-------
 .../jvarkit/vcfpolyx/tests/main.nf.test.snap  | 37 ++++++++
 4 files changed, 96 insertions(+), 97 deletions(-)
 create mode 100644 modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap

diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf
index 5a220cf31b5..6220fe9b163 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/main.nf
+++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf
@@ -1,89 +1,68 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process JVARKIT_VCFPOLYX {
-    tag '$bam'
+    tag "$meta.id"
     label 'process_single'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_0':
         'biocontainers/jvarkit:2024.08.25--hdfd78af_0' }"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    path bam
+    tuple val(meta),  path(vcf)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+    tuple val(meta4), path(dict)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    path "*.bam", emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.${extension}"), emit: vcf
+    tuple val(meta), path("*.tbi")         , emit: tbi, optional: true
+    tuple val(meta), path("*.csi")         , emit: csi, optional: true
+    path "versions.yml"                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    def args1  = task.ext.args1 ?: ''
+    def args2  = task.ext.args2 ?: ' --tag POLYX --max-repeats 10 '
+    def args3  = task.ext.args3 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    extension =     args3.contains("--output-type b") || args3.contains("-Ob") ? "bcf.gz" :
+                    args3.contains("--output-type u") || args3.contains("-Ou") ? "bcf" :
+                    args3.contains("--output-type z") || args3.contains("-Oz") ? "vcf.gz" :
+                    args3.contains("--output-type v") || args3.contains("-Ov") ? "vcf" :
+                    "vcf"
+
+    if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        $bam
+    set -o pipefail
+    mkdir -p TMP
+    
+    which bcftools || true && echo OK
+    
+    bcftools view -O v ${args1} "${vcf}" |\\
+	jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx --reference "${fasta}" ${args2} |\\
+        bcftools view --output "${prefix}.${extension}" ${args3}
+	
+    rm -rf TMP
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        jvarkit: \$(samtools --version |& sed '1!d ; s/samtools //')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        jvarkit: \$(jvarkit -v)
     END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.bam
+    touch "${prefix}.${extension}"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        jvarkit: \$(samtools --version |& sed '1!d ; s/samtools //')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        jvarkit: \$(jvarkit -v)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
index a2b1b3ead7f..36e92ed184c 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -19,7 +19,13 @@ tools:
 
 ## TODO nf-core: Add a description of all of the variables used as input
 input:
-  #
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  
   ## TODO nf-core: Delete / customise this example input
   - bam:
       type: file
@@ -28,7 +34,13 @@ input:
 
 ## TODO nf-core: Add a description of all of the variables used as output
 output:
-  #
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
index 93952cba65d..b98eba3f93e 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
+++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
@@ -1,4 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
 // nf-core modules test jvarkit/vcfpolyx
 nextflow_process {
 
@@ -11,20 +10,18 @@ nextflow_process {
     tag "jvarkit"
     tag "jvarkit/vcfpolyx"
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
-    test("sarscov2 - bam") {
-
-        // TODO nf-core: If you are created a test for a chained module
-        // (the module requires running more than one process to generate the required output)
-        // add the 'setup' method here.
-        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+    test("sarscov2 - vcf") {
 
         when {
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-                
-                input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                input[0] =[
+                    [id:"vcf_test"],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+                ]
+                input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
+                input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
+                input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
                 """
             }
         }
@@ -33,36 +30,10 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
             )
         }
 
     }
 
-    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
-    test("sarscov2 - bam - stub") {
-
-        options "-stub"
-
-        when {
-            process {
-                """
-                // TODO nf-core: define inputs of the process here. Example:
-                
-                input[0] = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-            )
-        }
-
-    }
 
 }
diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap
new file mode 100644
index 00000000000..71d0668813c
--- /dev/null
+++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+    "sarscov2 - vcf": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "csi": [
+                    
+                ],
+                "tbi": [
+                    
+                ],
+                "vcf": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-03T14:00:13.118369362"
+    }
+}
\ No newline at end of file

From 41ba2fc2fa159279c0c8593045c174dc76c34a99 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 12:02:39 +0200
Subject: [PATCH 03/16] vcfployx, tests ok

---
 .../nf-core/jvarkit/vcfpolyx/environment.yml  |  2 +-
 modules/nf-core/jvarkit/vcfpolyx/main.nf      | 13 +--
 modules/nf-core/jvarkit/vcfpolyx/meta.yml     | 80 ++++++++++++-------
 .../jvarkit/vcfpolyx/tests/main.nf.test       |  6 +-
 .../jvarkit/vcfpolyx/tests/main.nf.test.snap  | 32 ++------
 5 files changed, 68 insertions(+), 65 deletions(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
index 980e48236e6..04fc58514be 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
@@ -2,8 +2,8 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 name: "jvarkit_vcfpolyx"
 channels:
-  - conda-forge
   - bioconda
+  - conda-forge
   - defaults
 dependencies:
   - "bioconda::jvarkit=2024.08.25"
diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf
index 6220fe9b163..c0b594953a3 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/main.nf
+++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf
@@ -1,11 +1,16 @@
+/**
+ * JVARKIT_VCFPOLYX
+ * Author: Pierre Lindenbaum PhD
+ * vcfpolyx is a sub-command of the jvarkit package. It is used to annotate a vcf for the poly-x repeats
+ */
 process JVARKIT_VCFPOLYX {
     tag "$meta.id"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_0':
-        'biocontainers/jvarkit:2024.08.25--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_1':
+        'biocontainers/jvarkit:2024.08.25--hdfd78af_1' }"
 
     input:
     tuple val(meta),  path(vcf)
@@ -24,7 +29,7 @@ process JVARKIT_VCFPOLYX {
 
     script:
     def args1  = task.ext.args1 ?: ''
-    def args2  = task.ext.args2 ?: ' --tag POLYX --max-repeats 10 '
+    def args2  = meta.vcfpolyx_args ?: (task.ext.args2 ?: ' --tag POLYX --max-repeats 10 ')
     def args3  = task.ext.args3 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
@@ -39,8 +44,6 @@ process JVARKIT_VCFPOLYX {
     set -o pipefail
     mkdir -p TMP
     
-    which bcftools || true && echo OK
-    
     bcftools view -O v ${args1} "${vcf}" |\\
 	jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx --reference "${fasta}" ${args2} |\\
         bcftools view --output "${prefix}.${extension}" ${args3}
diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
index 36e92ed184c..ba1fd8edd80 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -1,55 +1,73 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "jvarkit_vcfpolyx"
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
+description: annotate VCF files for poly repeats
 keywords:
-  - sort
-  - example
-  - genomics
+  - vcf
+  - bcf
+  - annotation
+  - repeats
 tools:
+
   - "jvarkit":
-      ## TODO nf-core: Add a description and other details for the software below
       description: "Java utilities for Bioinformatics."
-      homepage: "None"
-      documentation: "None"
-      tool_dev_url: "None"
-      doi: ""
+      homepage: "https://github.com/lindenb/jvarkit"
+      documentation: "https://jvarkit.readthedocs.io/"
+      tool_dev_url: "https://github.com/lindenb/jvarkit"
+      doi: "http://dx.doi.org/10.6084/m9.figshare.1425030"
       licence: ['MIT License']
 
-## TODO nf-core: Add a description of all of the variables used as input
-input:
-  # Only when we have meta
-  - meta:
-      type: map
+  - "bcftools":
       description: |
-        Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
+        View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: http://www.htslib.org/doc/bcftools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+
+input:
+  - vcf:
+      type: file
+      description:   Groovy Map containing reference genome information for vcf
+      pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
+
+  - fasta:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description:  Groovy Map containing reference genome information for fai reference fasta file
+      pattern: "*.fasta"
+
+  - fai:
+      type: file
+      description:  Groovy Map containing reference genome information for fai
+      pattern: "*.fasta.fai"
+
+  - dict:
+      type: file
+      description:  Groovy Map containing reference genome information for GATK sequence dictionary
+      pattern: "*.dict"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
-  #Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
-        e.g. `[ id:'sample1', single_end:false ]`
-  
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF filtered output file
+      pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
+  - csi:
+      type: file
+      description: Default VCF file index
+      pattern: "*.csi"
+  - tbi:
+      type: file
+      description: Alternative VCF file index
+      pattern: "*.tbi"
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
-  - bam:
-      type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
 
 authors:
   - "@lindenb"
diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
index b98eba3f93e..72ec3a71473 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
+++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test
@@ -29,7 +29,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(
+					path(process.out.vcf[0][1]).vcf.variantsMD5,
+					process.out.versions
+					).match()
+			    }
             )
         }
 
diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap
index 71d0668813c..618902b4502 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap
+++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap
@@ -1,32 +1,10 @@
 {
     "sarscov2 - vcf": {
         "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "csi": [
-                    
-                ],
-                "tbi": [
-                    
-                ],
-                "vcf": [
-                    
-                ],
-                "versions": [
-                    
-                ]
-            }
+            "65a03a6057dc74467c2b7b17230e7f14",
+           [
+           "versions.yml:md5,dcb0bbe3f1b3aa091708acb0fb6361d5"
+           ] 
         ],
         "meta": {
             "nf-test": "0.9.0",
@@ -34,4 +12,4 @@
         },
         "timestamp": "2024-09-03T14:00:13.118369362"
     }
-}
\ No newline at end of file
+}

From 6a32597718ec5bc5b568b14f85bb5f8aab81a17e Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 12:33:51 +0200
Subject: [PATCH 04/16] fix env and meta ?

---
 modules/nf-core/jvarkit/vcfpolyx/environment.yml | 2 --
 modules/nf-core/jvarkit/vcfpolyx/meta.yml        | 8 ++++----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
index 04fc58514be..9ffce950e45 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
@@ -3,7 +3,5 @@
 name: "jvarkit_vcfpolyx"
 channels:
   - bioconda
-  - conda-forge
-  - defaults
 dependencies:
   - "bioconda::jvarkit=2024.08.25"
diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
index ba1fd8edd80..af2bb78a55f 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -14,15 +14,15 @@ tools:
       homepage: "https://github.com/lindenb/jvarkit"
       documentation: "https://jvarkit.readthedocs.io/"
       tool_dev_url: "https://github.com/lindenb/jvarkit"
-      doi: "http://dx.doi.org/10.6084/m9.figshare.1425030"
+      doi: "10.6084/m9.figshare.1425030"
       licence: ['MIT License']
 
   - "bcftools":
       description: |
         View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
-      homepage: http://samtools.github.io/bcftools/bcftools.html
-      documentation: http://www.htslib.org/doc/bcftools.html
-      doi: 10.1093/bioinformatics/btp352
+      homepage: "http://samtools.github.io/bcftools/bcftools.html"
+      documentation: "http://www.htslib.org/doc/bcftools.html"
+      doi: "10.1093/bioinformatics/btp352"
       licence: ["MIT"]
 
 input:

From 19a607992a77f36289f76a1de2b7960957241d64 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 12:40:22 +0200
Subject: [PATCH 05/16]  remove tab

---
 modules/nf-core/jvarkit/vcfpolyx/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf
index c0b594953a3..6afc27421ec 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/main.nf
+++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf
@@ -45,9 +45,9 @@ process JVARKIT_VCFPOLYX {
     mkdir -p TMP
     
     bcftools view -O v ${args1} "${vcf}" |\\
-	jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx --reference "${fasta}" ${args2} |\\
+        jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx --reference "${fasta}" ${args2} |\\
         bcftools view --output "${prefix}.${extension}" ${args3}
-	
+    
     rm -rf TMP
 
     cat <<-END_VERSIONS > versions.yml

From aa0eaeee267000e1a1b69e0d76e20f16d8bdbfe1 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 12:48:04 +0200
Subject: [PATCH 06/16] remove ws

---
 modules/nf-core/jvarkit/vcfpolyx/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf
index 6afc27421ec..ae4cec244d2 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/main.nf
+++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf
@@ -43,11 +43,11 @@ process JVARKIT_VCFPOLYX {
     """
     set -o pipefail
     mkdir -p TMP
-    
+
     bcftools view -O v ${args1} "${vcf}" |\\
         jvarkit -Xmx${task.memory.giga}g  -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx --reference "${fasta}" ${args2} |\\
         bcftools view --output "${prefix}.${extension}" ${args3}
-    
+
     rm -rf TMP
 
     cat <<-END_VERSIONS > versions.yml

From dceb14df6faa9634b97351e6f1ef71edf7597fe3 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Thu, 5 Sep 2024 10:38:08 +0000
Subject: [PATCH 07/16] [automated] Fix linting with Prettier

---
 modules/nf-core/jvarkit/vcfpolyx/meta.yml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
index af2bb78a55f..250168894cc 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -8,14 +8,13 @@ keywords:
   - annotation
   - repeats
 tools:
-
   - "jvarkit":
       description: "Java utilities for Bioinformatics."
       homepage: "https://github.com/lindenb/jvarkit"
       documentation: "https://jvarkit.readthedocs.io/"
       tool_dev_url: "https://github.com/lindenb/jvarkit"
       doi: "10.6084/m9.figshare.1425030"
-      licence: ['MIT License']
+      licence: ["MIT License"]
 
   - "bcftools":
       description: |
@@ -28,22 +27,22 @@ tools:
 input:
   - vcf:
       type: file
-      description:   Groovy Map containing reference genome information for vcf
+      description: Groovy Map containing reference genome information for vcf
       pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}"
 
   - fasta:
       type: file
-      description:  Groovy Map containing reference genome information for fai reference fasta file
+      description: Groovy Map containing reference genome information for fai reference fasta file
       pattern: "*.fasta"
 
   - fai:
       type: file
-      description:  Groovy Map containing reference genome information for fai
+      description: Groovy Map containing reference genome information for fai
       pattern: "*.fasta.fai"
 
   - dict:
       type: file
-      description:  Groovy Map containing reference genome information for GATK sequence dictionary
+      description: Groovy Map containing reference genome information for GATK sequence dictionary
       pattern: "*.dict"
 
 output:

From eef5c98b4c728c758a798e01cf59fdcec9e3cfc0 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 12:55:09 +0200
Subject: [PATCH 08/16] fix conda ?

---
 modules/nf-core/jvarkit/vcfpolyx/environment.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
index 9ffce950e45..04fc58514be 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
@@ -3,5 +3,7 @@
 name: "jvarkit_vcfpolyx"
 channels:
   - bioconda
+  - conda-forge
+  - defaults
 dependencies:
   - "bioconda::jvarkit=2024.08.25"

From 801698a94784ae17b0c47c671e1a9cf518bec6ce Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 13:48:32 +0200
Subject: [PATCH 09/16] remove defaults

---
 modules/nf-core/jvarkit/vcfpolyx/environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
index 04fc58514be..cf7e84012ee 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml
@@ -4,6 +4,5 @@ name: "jvarkit_vcfpolyx"
 channels:
   - bioconda
   - conda-forge
-  - defaults
 dependencies:
   - "bioconda::jvarkit=2024.08.25"

From 797639a885e32b143e20e13fdd59302b0613f1eb Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 14:02:42 +0200
Subject: [PATCH 10/16] fix meta info

---
 modules/nf-core/jvarkit/vcfpolyx/meta.yml | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
index 250168894cc..bb915a543cd 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -25,6 +25,22 @@ tools:
       licence: ["MIT"]
 
 input:
+  -meta:
+      description: |
+        Groovy Map containing VCF information
+
+  -meta2:
+      description: |
+        Groovy Map containing fasta information
+
+  -meta2:
+      description: |
+        Groovy Map containing fasta.fai information
+
+  -meta3:
+      description: |
+        Groovy Map containing fasta.dict information
+
   - vcf:
       type: file
       description: Groovy Map containing reference genome information for vcf
@@ -49,7 +65,7 @@ output:
   - meta:
       type: map
       description: |
-        Groovy Map containing sample information
+        Groovy Map containing VCF information
         e.g. [ id:'test', single_end:false ]
   - vcf:
       type: file

From 0acd7af7984c828d5b8a68f09d93f1a51635136b Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 14:13:10 +0200
Subject: [PATCH 11/16] I hate myslef, fix warnings

---
 modules/nf-core/jvarkit/vcfpolyx/meta.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
index bb915a543cd..d3d56b75bc1 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -25,19 +25,19 @@ tools:
       licence: ["MIT"]
 
 input:
-  -meta:
+  - meta:
       description: |
         Groovy Map containing VCF information
 
-  -meta2:
+  - meta2:
       description: |
         Groovy Map containing fasta information
 
-  -meta2:
+  - meta2:
       description: |
         Groovy Map containing fasta.fai information
 
-  -meta3:
+  - meta3:
       description: |
         Groovy Map containing fasta.dict information
 

From 4064e3c60f02fc142ef7ef440b5b74c286e29ba5 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 14:19:15 +0200
Subject: [PATCH 12/16] add type to meta

---
 modules/nf-core/jvarkit/vcfpolyx/meta.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
index d3d56b75bc1..10bcfdd1188 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -26,18 +26,22 @@ tools:
 
 input:
   - meta:
+      type: map
       description: |
         Groovy Map containing VCF information
 
   - meta2:
+      type: map
       description: |
         Groovy Map containing fasta information
 
   - meta2:
+      type: map
       description: |
         Groovy Map containing fasta.fai information
 
   - meta3:
+      type: map
       description: |
         Groovy Map containing fasta.dict information
 

From 67e6c915396b6e8a190c8c2228fd9eee21610575 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 14:51:30 +0200
Subject: [PATCH 13/16] fix snap md5

---
 modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap
index 618902b4502..e5ccf191472 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap
+++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap
@@ -3,7 +3,7 @@
         "content": [
             "65a03a6057dc74467c2b7b17230e7f14",
            [
-           "versions.yml:md5,dcb0bbe3f1b3aa091708acb0fb6361d5"
+           "versions.yml:md5,b3c351a56da9062295ef90011a9cd48c"
            ] 
         ],
         "meta": {

From 75b3a9afeead6f97fabf05f75b64c616d3123801 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 15:19:50 +0200
Subject: [PATCH 14/16] fix meta3/meta4
 https://github.com/nf-core/modules/pull/6580#discussion_r1745494016

---
 modules/nf-core/jvarkit/vcfpolyx/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
index 10bcfdd1188..221f7e9ca51 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml
+++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml
@@ -35,12 +35,12 @@ input:
       description: |
         Groovy Map containing fasta information
 
-  - meta2:
+  - meta3:
       type: map
       description: |
         Groovy Map containing fasta.fai information
 
-  - meta3:
+  - meta4:
       type: map
       description: |
         Groovy Map containing fasta.dict information

From 8b2115a740fde92a9bc612a9a9361a6251429cf4 Mon Sep 17 00:00:00 2001
From: lindenb <plindenbaum@yahoo.fr>
Date: Thu, 5 Sep 2024 15:34:11 +0200
Subject: [PATCH 15/16] fix
 https://github.com/nf-core/modules/pull/6580#discussion_r1745463698

---
 modules/nf-core/jvarkit/vcfpolyx/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf
index ae4cec244d2..9ae4269bae0 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/main.nf
+++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf
@@ -41,7 +41,6 @@ process JVARKIT_VCFPOLYX {
 
     if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
     """
-    set -o pipefail
     mkdir -p TMP
 
     bcftools view -O v ${args1} "${vcf}" |\\

From da213ab4bbe95a8ca37cd42f7ff4d3a66bf1cfd0 Mon Sep 17 00:00:00 2001
From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com>
Date: Thu, 5 Sep 2024 15:40:56 +0200
Subject: [PATCH 16/16] Update modules/nf-core/jvarkit/vcfpolyx/main.nf

Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
---
 modules/nf-core/jvarkit/vcfpolyx/main.nf | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf
index 9ae4269bae0..77005f6fc46 100644
--- a/modules/nf-core/jvarkit/vcfpolyx/main.nf
+++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf
@@ -1,8 +1,3 @@
-/**
- * JVARKIT_VCFPOLYX
- * Author: Pierre Lindenbaum PhD
- * vcfpolyx is a sub-command of the jvarkit package. It is used to annotate a vcf for the poly-x repeats
- */
 process JVARKIT_VCFPOLYX {
     tag "$meta.id"
     label 'process_single'