From c093611bbb56281f4b1f9f2f1590ef85416ff7b0 Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Mon, 17 Jun 2024 10:01:29 +0200
Subject: [PATCH 1/8] sort raw vcf

---
 .gitignore                             |  2 ++
 modules/local/file_concatenator.nf     |  4 +--
 modules/local/sort_nonstandard_vcf.nf  | 38 ++++++++++++++++++++++++++
 run_pipeline.sh                        |  2 +-
 subworkflows/local/mpileup_snv_call.nf | 13 ++++++++-
 5 files changed, 55 insertions(+), 4 deletions(-)
 create mode 100644 modules/local/sort_nonstandard_vcf.nf

diff --git a/.gitignore b/.gitignore
index a9cfb02..bc7f825 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,6 +11,7 @@ __pycache__
 output/
 results/
 result/
+results2/
 results37/
 test.xml
 test_output/
@@ -19,3 +20,4 @@ work/
 testdata_hg37/
 .github/CODEOWNERS-tmp
 bin/vcfparser.pyc
+singularity/
diff --git a/modules/local/file_concatenator.nf b/modules/local/file_concatenator.nf
index 678ab24..c3602aa 100644
--- a/modules/local/file_concatenator.nf
+++ b/modules/local/file_concatenator.nf
@@ -21,9 +21,9 @@ process FILE_CONCATENATOR {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    headeredFileConcatenator.pl $vcfs > snvs_${prefix}_raw.vcf
+    headeredFileConcatenator.pl $vcfs > snvs_${prefix}.vcf
 
-    bgzip snvs_${prefix}_raw.vcf && tabix -p vcf snvs_${prefix}_raw.vcf.gz 
+    bgzip snvs_${prefix}.vcf && tabix -p vcf snvs_${prefix}.vcf.gz 
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/sort_nonstandard_vcf.nf b/modules/local/sort_nonstandard_vcf.nf
new file mode 100644
index 0000000..0321aaa
--- /dev/null
+++ b/modules/local/sort_nonstandard_vcf.nf
@@ -0,0 +1,38 @@
+process SORT_NONSTANDARD_VCF {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda (params.enable_conda ? "" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'docker://kubran/odcf_mpileupsnvcalling:v0':'kubran/odcf_mpileupsnvcalling:v0' }"
+
+    input:
+    tuple val(meta), path(vcf_gz), path(index)
+
+    output:
+    tuple val(meta), path("*_raw.vcf.gz"),path("*_raw.vcf.gz.tbi")  , emit: output
+    path "versions.yml"                                             , emit: versions
+
+    script: 
+    def args       = task.ext.args ?: ''
+    def prefix     = task.ext.prefix ?: "${meta.id}"
+    
+
+    """
+    bgzip -d $vcf_gz >  temp.vcf
+
+    (head -n 5000 temp.vcf | \\
+        grep "#" ; cat temp.vcf | \\
+        grep -v "#" | \\
+        sort -T . -k1,1V -n -k2,2n ) > temp_sorted.vcf
+
+    bgzip temp_sorted.vcf > snvs_${prefix}_sorted.vcf.gz
+    tabix -p vcf snvs_${prefix}_sorted.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools 2>&1) | sed -e 's/.*Version: //; s/ Usage.*//')
+    END_VERSIONS
+    """
+    
+}
\ No newline at end of file
diff --git a/run_pipeline.sh b/run_pipeline.sh
index 5ce5fac..82fb564 100644
--- a/run_pipeline.sh
+++ b/run_pipeline.sh
@@ -1,3 +1,3 @@
 #!/bin/bash
 module load nextflow/22.07.1-edge
-nextflow run main.nf -profile dkfz_cluster_hg38,singularity --outdir results
\ No newline at end of file
+nextflow run main.nf -profile dkfz_cluster_hg38,singularity --outdir results2 --input assets/samplesheet_hg38_WGS.csv -resume
\ No newline at end of file
diff --git a/subworkflows/local/mpileup_snv_call.nf b/subworkflows/local/mpileup_snv_call.nf
index 125d0b0..417108f 100644
--- a/subworkflows/local/mpileup_snv_call.nf
+++ b/subworkflows/local/mpileup_snv_call.nf
@@ -8,6 +8,7 @@ include { BCFTOOLS_MPILEUP      } from '../../modules/nf-core/modules/bcftools/m
 include { MPILEUP_COMPARE       } from '../../modules/local/mpileup_compare.nf'               addParams( options: params.options )
 include { SEQ_CONTEXT_ANNOTATOR } from '../../modules/local/seq_context_annotator.nf'         addParams( options: params.options )
 include { FILE_CONCATENATOR     } from '../../modules/local/file_concatenator.nf'             addParams( options: params.options )
+include { SORT_NONSTANDARD_VCF  } from '../../modules/local/sort_nonstandard_vcf.nf'          addParams( options: params.options )
 
 
 workflow MPILEUP_SNV_CALL {
@@ -120,7 +121,17 @@ workflow MPILEUP_SNV_CALL {
         combined_vcf
     )
     versions = versions.mix(FILE_CONCATENATOR.out.versions) 
-    vcf_ch=FILE_CONCATENATOR.out.vcf
+
+    // 
+    // MODULE: SORT_NONSTANDARD_VCF
+    //
+    // Sort raw file
+    SORT_NONSTANDARD_VCF(
+        FILE_CONCATENATOR.out.vcf
+    )
+    versions = versions.mix(SORT_NONSTANDARD_VCF.out.versions) 
+    vcf_ch=SORT_NONSTANDARD_VCF.out.output
+
 
     emit:
     vcf_ch

From b89418c88620cdd3723d9b0610a2f89b80a5b768 Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Mon, 17 Jun 2024 16:37:10 +0200
Subject: [PATCH 2/8] docker changed

---
 modules/local/sort_nonstandard_vcf.nf | 14 +++++---------
 1 file changed, 5 insertions(+), 9 deletions(-)

diff --git a/modules/local/sort_nonstandard_vcf.nf b/modules/local/sort_nonstandard_vcf.nf
index 0321aaa..5cb6a4e 100644
--- a/modules/local/sort_nonstandard_vcf.nf
+++ b/modules/local/sort_nonstandard_vcf.nf
@@ -4,7 +4,7 @@ process SORT_NONSTANDARD_VCF {
 
     conda (params.enable_conda ? "" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'docker://kubran/odcf_mpileupsnvcalling:v0':'kubran/odcf_mpileupsnvcalling:v0' }"
+        'docker://kubran/samtools:v1.9':'kubran/samtools:v1.9' }"
 
     input:
     tuple val(meta), path(vcf_gz), path(index)
@@ -17,17 +17,13 @@ process SORT_NONSTANDARD_VCF {
     def args       = task.ext.args ?: ''
     def prefix     = task.ext.prefix ?: "${meta.id}"
     
-
     """
-    bgzip -d $vcf_gz >  temp.vcf
-
-    (head -n 5000 temp.vcf | \\
-        grep "#" ; cat temp.vcf | \\
+    (zcat $vcf_gz | head -n 5000 | \\
+        grep "#" ; zcat $vcf_gz | \\
         grep -v "#" | \\
-        sort -T . -k1,1V -n -k2,2n ) > temp_sorted.vcf
+        sort -T . -k1,1V -k2,2n ) | bgzip > snvs_${prefix}_raw.vcf.gz
 
-    bgzip temp_sorted.vcf > snvs_${prefix}_sorted.vcf.gz
-    tabix -p vcf snvs_${prefix}_sorted.vcf.gz
+    tabix -p vcf snvs_${prefix}_raw.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From ff6fd9f504e3d5c9455ac16316f71aefc1cdc2f6 Mon Sep 17 00:00:00 2001
From: kubranarci <kbrnrc@gmail.com>
Date: Thu, 20 Jun 2024 15:12:12 +0200
Subject: [PATCH 3/8] fix sorting pipe

---
 assets/samplesheet_hg38_WGS.csv        | 3 +--
 modules/local/seq_context_annotator.nf | 7 ++-----
 modules/local/sort_nonstandard_vcf.nf  | 9 ++++-----
 3 files changed, 7 insertions(+), 12 deletions(-)

diff --git a/assets/samplesheet_hg38_WGS.csv b/assets/samplesheet_hg38_WGS.csv
index 1867eb4..5b241fd 100644
--- a/assets/samplesheet_hg38_WGS.csv
+++ b/assets/samplesheet_hg38_WGS.csv
@@ -1,3 +1,2 @@
 sample,tumor,tumor_index,control,control_index
-SEQC2_LL1,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/tumor01_SEQC2_LL1_merged.mdup.bam,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/tumor01_SEQC2_LL1_merged.mdup.bam.bai,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/control01_SEQC2_LL1_merged.mdup.bam,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/control01_SEQC2_LL1_merged.mdup.bam.bai
-SEQC2_LL2,/omics/odcf/project/public_data/seqc2/sequencing/whole_genome_sequencing/view-by-pid/SEQC2_IL2/tumor01/paired/merged-alignment/tumor01_SEQC2_IL2_merged.mdup.bam,/omics/odcf/project/public_data/seqc2/sequencing/whole_genome_sequencing/view-by-pid/SEQC2_IL2/tumor01/paired/merged-alignment/tumor01_SEQC2_IL2_merged.mdup.bam.bai,/omics/odcf/project/public_data/seqc2/sequencing/whole_genome_sequencing/view-by-pid/SEQC2_IL2/control01/paired/merged-alignment/control01_SEQC2_IL2_merged.mdup.bam,/omics/odcf/project/public_data/seqc2/sequencing/whole_genome_sequencing/view-by-pid/SEQC2_IL2/control01/paired/merged-alignment/control01_SEQC2_IL2_merged.mdup.bam.bai
\ No newline at end of file
+SEQC2_LL1,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/tumor01_SEQC2_LL1_merged.mdup.bam,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/tumor01_SEQC2_LL1_merged.mdup.bam.bai,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/control01_SEQC2_LL1_merged.mdup.bam,/omics/odcf/analysis/OE0526_projects/public_data_analyses/seqc2/sequencing/whole_genome_sequencing/results_per_pid/SEQC2_LL1/alignment/control01_SEQC2_LL1_merged.mdup.bam.bai
\ No newline at end of file
diff --git a/modules/local/seq_context_annotator.nf b/modules/local/seq_context_annotator.nf
index 1cc1393..5e46085 100644
--- a/modules/local/seq_context_annotator.nf
+++ b/modules/local/seq_context_annotator.nf
@@ -26,11 +26,8 @@ process SEQ_CONTEXT_ANNOTATOR {
     """
     seqContext_annotator.pl fastaFromBed $vcf $fasta 10 | \\
         rawSnvFilter.py --outf=${prefix}.${intervals}.bias.vcf.temp $args
-    
-    (head -n 5000 ${prefix}.${intervals}.bias.vcf.temp | \\
-        grep "#" ; cat ${prefix}.${intervals}.bias.vcf.temp | \\
-        grep -v "#" | \\
-        sort -T . -k1,1V -n -k2,2n ) > ${prefix}.${intervals}.bias.vcf
+
+    awk '/^#/ {print; next} {print | "sort -T . -k1,1V -k2,2n"}' ${prefix}.${intervals}.bias.vcf.temp > ${prefix}.${intervals}.bias.vcf
 
     bcftools stats ${prefix}.${intervals}.bias.vcf > ${prefix}.${intervals}.bias.bcftools_stats.txt
 
diff --git a/modules/local/sort_nonstandard_vcf.nf b/modules/local/sort_nonstandard_vcf.nf
index 5cb6a4e..aba1c50 100644
--- a/modules/local/sort_nonstandard_vcf.nf
+++ b/modules/local/sort_nonstandard_vcf.nf
@@ -18,16 +18,15 @@ process SORT_NONSTANDARD_VCF {
     def prefix     = task.ext.prefix ?: "${meta.id}"
     
     """
-    (zcat $vcf_gz | head -n 5000 | \\
-        grep "#" ; zcat $vcf_gz | \\
-        grep -v "#" | \\
-        sort -T . -k1,1V -k2,2n ) | bgzip > snvs_${prefix}_raw.vcf.gz
+    zcat $vcf_gz | \
+    awk 'BEGIN {header=1} /^#/ {print; next} {header=0; print | "sort -T . -k1,1V -k2,2n"}' | \
+    bgzip > snvs_${prefix}_raw.vcf.gz
 
     tabix -p vcf snvs_${prefix}_raw.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        samtools: \$(echo \$(samtools 2>&1) | sed -e 's/.*Version: //; s/ Usage.*//')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
     

From 459c4207b4adc494e578963a19b29754be0d432b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Thu, 20 Jun 2024 14:38:39 +0000
Subject: [PATCH 4/8] run on singularity

---
 .github/workflows/main.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index f64d02f..2cf3a2d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -39,9 +39,9 @@ jobs:
       - name: DELAY to try address some odd behaviour with what appears to be a conflict between parallel htslib jobs leading to CI hangs
         run: |
           if [[ $NXF_VER = '' ]]; then sleep 1200; fi
-      - name: BASIC Run the basic pipeline  with docker
+      - name: BASIC Run the basic pipeline  with singularity
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity
       - name: BASIC Run the basic pipeline when --runcontig set to "ALT_HLA" (contigs does not exist in bam)
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --runcontigs "ALT_HLA"
\ No newline at end of file
+          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --runcontigs "ALT_HLA"
\ No newline at end of file

From c96c5393ef54b4224aa509716cf95388f6659cbb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Thu, 20 Jun 2024 15:09:04 +0000
Subject: [PATCH 5/8] back to docker

---
 .github/workflows/main.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2cf3a2d..f64d02f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -39,9 +39,9 @@ jobs:
       - name: DELAY to try address some odd behaviour with what appears to be a conflict between parallel htslib jobs leading to CI hangs
         run: |
           if [[ $NXF_VER = '' ]]; then sleep 1200; fi
-      - name: BASIC Run the basic pipeline  with singularity
+      - name: BASIC Run the basic pipeline  with docker
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
       - name: BASIC Run the basic pipeline when --runcontig set to "ALT_HLA" (contigs does not exist in bam)
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --runcontigs "ALT_HLA"
\ No newline at end of file
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --runcontigs "ALT_HLA"
\ No newline at end of file

From 286faf0aa0b288adc69c26bfa23ca074e951e036 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Fri, 21 Jun 2024 12:06:33 +0000
Subject: [PATCH 6/8] bcftools docker new image

---
 .../nf-core/modules/bcftools/mpileup/main.nf  |   3 +-
 .../modules/bcftools/reheader/environment.yml |   7 -
 .../nf-core/modules/bcftools/reheader/main.nf |  74 -------
 .../modules/bcftools/reheader/meta.yml        |  63 ------
 .../bcftools/reheader/tests/bcf.config        |   4 -
 .../bcftools/reheader/tests/main.nf.test      | 197 ------------------
 .../bcftools/reheader/tests/main.nf.test.snap | 166 ---------------
 .../modules/bcftools/reheader/tests/tags.yml  |   2 -
 .../bcftools/reheader/tests/vcf.config        |   4 -
 .../bcftools/reheader/tests/vcf.gz.config     |   4 -
 modules/nf-core/modules/bcftools/sort/main.nf |   3 +-
 11 files changed, 2 insertions(+), 525 deletions(-)
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/environment.yml
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/main.nf
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/meta.yml
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/tests/bcf.config
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/tests/main.nf.test
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/tests/main.nf.test.snap
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/tests/tags.yml
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/tests/vcf.config
 delete mode 100644 modules/nf-core/modules/bcftools/reheader/tests/vcf.gz.config

diff --git a/modules/nf-core/modules/bcftools/mpileup/main.nf b/modules/nf-core/modules/bcftools/mpileup/main.nf
index 263311c..a2f02e3 100644
--- a/modules/nf-core/modules/bcftools/mpileup/main.nf
+++ b/modules/nf-core/modules/bcftools/mpileup/main.nf
@@ -4,8 +4,7 @@ process BCFTOOLS_MPILEUP {
 
     conda (params.enable_conda ? "bioconda::bcftools=1.9" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.9--h47928c2_2':
-        'quay.io/biocontainers/bcftools:1.9--h47928c2_2' }"
+        'docker://kubran/bcftools:1.9':'kubran/bcftools:1.9' }"
 
     input:
     tuple val(meta), path(tumor), path(tumor_bai), path(control),  path(control_bai), val(tumorname), val(controlname), val(intervals), path(interval_file)
diff --git a/modules/nf-core/modules/bcftools/reheader/environment.yml b/modules/nf-core/modules/bcftools/reheader/environment.yml
deleted file mode 100644
index aab0dc9..0000000
--- a/modules/nf-core/modules/bcftools/reheader/environment.yml
+++ /dev/null
@@ -1,7 +0,0 @@
-name: bcftools_reheader
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::bcftools=1.18
diff --git a/modules/nf-core/modules/bcftools/reheader/main.nf b/modules/nf-core/modules/bcftools/reheader/main.nf
deleted file mode 100644
index 25716cb..0000000
--- a/modules/nf-core/modules/bcftools/reheader/main.nf
+++ /dev/null
@@ -1,74 +0,0 @@
-process BCFTOOLS_REHEADER {
-    tag "$meta.id"
-    label 'process_low'
-
-    //conda "${moduleDir}/environment.yml"
-    conda (params.enable_conda ? "${moduleDir}/environment.yml" : null)
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
-        'quay.io/biocontainers/bcftools:1.18--h8b25389_0' }"
-
-    input:
-    tuple val(meta), path(vcf), path(header), path(samples)
-    tuple val(meta2), path(fai)
-
-    output:
-    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
-    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 fai_argument      = fai ? "--fai $fai" : ""
-    def header_argument   = header ? "--header $header" : ""
-    def samples_argument  = samples ? "--samples $samples" : ""
-
-    def args2 = task.ext.args2 ?: '--output-type z'
-    def extension = args2.contains("--output-type b") || args2.contains("-Ob") ? "bcf.gz" :
-                    args2.contains("--output-type u") || args2.contains("-Ou") ? "bcf" :
-                    args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" :
-                    args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" :
-                    "vcf"
-    def vcf_name = vcf.getExtension() == "gz" ? vcf.getBaseName() : vcf.getName()
-    vcf_name = vcf_name.take(vcf_name.size() - 4)
-
-    """
-    bcftools \\
-        reheader \\
-        $fai_argument \\
-        $header_argument \\
-        $samples_argument \\
-        $args \\
-        --threads $task.cpus \\
-        $vcf \\
-        | bcftools view \\
-        $args2 \\
-        --output ${vcf_name}.header.${extension}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
-    END_VERSIONS
-    """
-
-    stub:
-    def args2 = task.ext.args2 ?: '--output-type z'
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    def extension = args2.contains("--output-type b") || args2.contains("-Ob") ? "bcf.gz" :
-                    args2.contains("--output-type u") || args2.contains("-Ou") ? "bcf" :
-                    args2.contains("--output-type z") || args2.contains("-Oz") ? "vcf.gz" :
-                    args2.contains("--output-type v") || args2.contains("-Ov") ? "vcf" :
-                    "vcf"
-    """
-    touch ${prefix}.${extension}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/modules/bcftools/reheader/meta.yml b/modules/nf-core/modules/bcftools/reheader/meta.yml
deleted file mode 100644
index 690d4ea..0000000
--- a/modules/nf-core/modules/bcftools/reheader/meta.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-name: bcftools_reheader
-description: Reheader a VCF file
-keywords:
-  - reheader
-  - vcf
-  - update header
-tools:
-  - reheader:
-      description: |
-        Modify header of VCF/BCF files, change sample names.
-      homepage: http://samtools.github.io/bcftools/bcftools.html
-      documentation: http://samtools.github.io/bcftools/bcftools.html#reheader
-      doi: 10.1093/gigascience/giab008
-      licence: ["MIT"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - vcf:
-      type: file
-      description: VCF/BCF file
-      pattern: "*.{vcf.gz,vcf,bcf}"
-  - header:
-      type: file
-      description: New header to add to the VCF
-      pattern: "*.{header.txt}"
-  - samples:
-      type: file
-      description: File containing sample names to update (one sample per line)
-      pattern: "*.{samples.txt}"
-  - meta2:
-      type: map
-      description: |
-        Groovy Map containing reference information
-        e.g. [ id:'genome' ]
-  - fai:
-      type: file
-      description: Fasta index to update header sequences with
-      pattern: "*.{fai}"
-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"
-  - vcf:
-      type: file
-      description: VCF with updated header, bgzipped per default
-      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
-authors:
-  - "@bjohnnyd"
-  - "@jemten"
-  - "@ramprasadn"
-maintainers:
-  - "@bjohnnyd"
-  - "@jemten"
-  - "@ramprasadn"
diff --git a/modules/nf-core/modules/bcftools/reheader/tests/bcf.config b/modules/nf-core/modules/bcftools/reheader/tests/bcf.config
deleted file mode 100644
index 2b7dff5..0000000
--- a/modules/nf-core/modules/bcftools/reheader/tests/bcf.config
+++ /dev/null
@@ -1,4 +0,0 @@
-process {
-    ext.args2 = { "--no-version --output-type b" }
-    ext.prefix = "tested"
-}
\ No newline at end of file
diff --git a/modules/nf-core/modules/bcftools/reheader/tests/main.nf.test b/modules/nf-core/modules/bcftools/reheader/tests/main.nf.test
deleted file mode 100644
index f3200cb..0000000
--- a/modules/nf-core/modules/bcftools/reheader/tests/main.nf.test
+++ /dev/null
@@ -1,197 +0,0 @@
-nextflow_process {
-
-    name "Test Process BCFTOOLS_REHEADER"
-    script "../main.nf"
-    process "BCFTOOLS_REHEADER"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "bcftools"
-    tag "bcftools/reheader"
-
-    test("sarscov2 - [vcf, [], []], fai - vcf output") {
-
-        config "./vcf.config"
-        when {
-
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    [],
-                    []
-                ]
-                input[1] = [ 
-                    [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - [vcf, [], []], fai - vcf.gz output") {
-
-        config "./vcf.gz.config"
-        when {
-
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    [],
-                    []
-                ]
-                input[1] = [ 
-                    [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - [vcf, [], []], fai - bcf output") {
-
-        config "./bcf.config"
-        when {
-
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    [],
-                    []
-                ]
-                input[1] = [ 
-                    [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - [vcf, header, []], []") {
-
-        config "./vcf.config"
-        when {
-
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
-                    []
-                ]
-                input[1] = [ 
-                    [ id:'genome' ], // meta map
-                    []
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - [vcf, [], samples], fai") {
-
-        config "./vcf.config"
-        when {
-
-            process {
-                """
-                ch_no_samples = Channel.of([
-                    [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    []
-                ])
-                ch_samples = Channel.of(["samples.txt", "new_name"])
-                    .collectFile(newLine:true)
-                input[0] = ch_no_samples.combine(ch_samples)
-                input[1] = [ 
-                    [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("sarscov2 - [vcf, [], []], fai - stub") {
-
-        options "-stub"
-        config "./vcf.config"
-        when {
-
-            process {
-                """
-                input[0] = [
-                    [ id:'test', single_end:false ],
-                    file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                    [],
-                    []
-                ]
-                input[1] = [ 
-                    [ id:'genome' ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    file(process.out.vcf[0][1]).name,
-                    process.out.versions,
-                ).match() }
-            )
-        }
-
-    }
-
-}
diff --git a/modules/nf-core/modules/bcftools/reheader/tests/main.nf.test.snap b/modules/nf-core/modules/bcftools/reheader/tests/main.nf.test.snap
deleted file mode 100644
index 112736a..0000000
--- a/modules/nf-core/modules/bcftools/reheader/tests/main.nf.test.snap
+++ /dev/null
@@ -1,166 +0,0 @@
-{
-    "sarscov2 - [vcf, [], []], fai - vcf output": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.vcf:md5,8e722884ffb75155212a3fc053918766"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.vcf:md5,8e722884ffb75155212a3fc053918766"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-29T13:05:44.058376693"
-    },
-    "sarscov2 - [vcf, [], []], fai - bcf output": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.bcf.gz:md5,c31d9afd8614832c2a46d9a55682c97a"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.bcf.gz:md5,c31d9afd8614832c2a46d9a55682c97a"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-29T13:06:03.793372514"
-    },
-    "sarscov2 - [vcf, [], []], fai - vcf.gz output": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.vcf.gz:md5,a1e45fe6d2b386fc2611766e5d2937ee"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.vcf.gz:md5,a1e45fe6d2b386fc2611766e5d2937ee"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-29T13:05:53.954090441"
-    },
-    "sarscov2 - [vcf, [], []], fai - stub": {
-        "content": [
-            "tested.vcf",
-            [
-                "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-            ]
-        ],
-        "timestamp": "2023-11-29T13:06:33.549685303"
-    },
-    "sarscov2 - [vcf, [], samples], fai": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.vcf:md5,c64c373c10b0be24b29d6f18708ec1e8"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.vcf:md5,c64c373c10b0be24b29d6f18708ec1e8"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-29T13:06:23.474745156"
-    },
-    "sarscov2 - [vcf, header, []], []": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.vcf:md5,3189bc9a720d5d5d3006bf72d91300cb"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "tested.vcf:md5,3189bc9a720d5d5d3006bf72d91300cb"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,fbf8ac8da771b6295a47392003f983ce"
-                ]
-            }
-        ],
-        "timestamp": "2023-11-29T13:06:13.841648691"
-    }
-}
\ No newline at end of file
diff --git a/modules/nf-core/modules/bcftools/reheader/tests/tags.yml b/modules/nf-core/modules/bcftools/reheader/tests/tags.yml
deleted file mode 100644
index c252941..0000000
--- a/modules/nf-core/modules/bcftools/reheader/tests/tags.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-bcftools/reheader:
-  - modules/nf-core/bcftools/reheader/**
diff --git a/modules/nf-core/modules/bcftools/reheader/tests/vcf.config b/modules/nf-core/modules/bcftools/reheader/tests/vcf.config
deleted file mode 100644
index 820f2ae..0000000
--- a/modules/nf-core/modules/bcftools/reheader/tests/vcf.config
+++ /dev/null
@@ -1,4 +0,0 @@
-process {
-    ext.args2 = { "--no-version" }
-    ext.prefix = "tested"
-}
\ No newline at end of file
diff --git a/modules/nf-core/modules/bcftools/reheader/tests/vcf.gz.config b/modules/nf-core/modules/bcftools/reheader/tests/vcf.gz.config
deleted file mode 100644
index c3031c3..0000000
--- a/modules/nf-core/modules/bcftools/reheader/tests/vcf.gz.config
+++ /dev/null
@@ -1,4 +0,0 @@
-process {
-    ext.args2 = { "--no-version --output-type z" }
-    ext.prefix = "tested"
-}
\ No newline at end of file
diff --git a/modules/nf-core/modules/bcftools/sort/main.nf b/modules/nf-core/modules/bcftools/sort/main.nf
index ef2513f..3b9e5c2 100644
--- a/modules/nf-core/modules/bcftools/sort/main.nf
+++ b/modules/nf-core/modules/bcftools/sort/main.nf
@@ -5,8 +5,7 @@ process BCFTOOLS_SORT {
     //conda "${moduleDir}/environment.yml"
     conda (params.enable_conda ? "${moduleDir}/environment.yml" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bcftools:1.18--h8b25389_0':
-        'quay.io/biocontainers/bcftools:1.18--h8b25389_0' }"
+        'docker://kubran/bcftools:1.9':'kubran/bcftools:1.9' }"
 
     input:
     tuple val(meta), path(vcf), path(index)

From 7187c57f6e17dce2240ad1fe9965d3582768938b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Fri, 21 Jun 2024 13:14:29 +0000
Subject: [PATCH 7/8] --output-file

---
 modules/nf-core/modules/bcftools/sort/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/modules/bcftools/sort/main.nf b/modules/nf-core/modules/bcftools/sort/main.nf
index 3b9e5c2..993b97e 100644
--- a/modules/nf-core/modules/bcftools/sort/main.nf
+++ b/modules/nf-core/modules/bcftools/sort/main.nf
@@ -31,7 +31,7 @@ process BCFTOOLS_SORT {
     """
     bcftools \\
         sort \\
-        --output ${vcf_name}.sorted.${extension} \\
+        --output-file ${vcf_name}.sorted.${extension} \\
         --temp-dir . \\
         $args \\
         $vcf

From d456009e472ec4b65c3fae3694141422327014c5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?K=C3=BCbra=20Narc=C4=B1?= <kbrnrc@gmail.com>
Date: Mon, 24 Jun 2024 10:09:31 +0200
Subject: [PATCH 8/8] outputs

---
 .github/workflows/main.yml |  5 +----
 conf/modules.config        | 10 ++--------
 2 files changed, 3 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index f64d02f..61f767d 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -41,7 +41,4 @@ jobs:
           if [[ $NXF_VER = '' ]]; then sleep 1200; fi
       - name: BASIC Run the basic pipeline  with docker
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
-      - name: BASIC Run the basic pipeline when --runcontig set to "ALT_HLA" (contigs does not exist in bam)
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --runcontigs "ALT_HLA"
\ No newline at end of file
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
\ No newline at end of file
diff --git a/conf/modules.config b/conf/modules.config
index d3cc3d7..a32597d 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -64,7 +64,7 @@ process {
             mode: params.publish_dir_mode
         ]
     }
-    withName: FILE_CONCATENATOR {
+    withName: SORT_NONSTANDARD_VCF {
         publishDir = [
             path: {"${params.outdir}/${meta.id}"},
             pattern: "*{.vcf.gz,vcf.gz.tbi}",
@@ -175,12 +175,6 @@ process {
             ]
         ]
     }
-        withName: 'CONVERT_TO_VCF' {
-        publishDir = [
-            path: { "${params.outdir}/test" },
-            enabled: false
-        ]
-    }  
     withName: 'BCFTOOLS_SORT' {
         publishDir = [
             path: { "${params.outdir}/${meta.id}/standard_vcf/" },
@@ -199,7 +193,7 @@ process {
 // Don't publish results for these processes
 //
 process {    
-    withName: 'GREP_SAMPLENAME|ANNOVAR|MUTATION_DISTANCE|CONTEXT_FREQUENCIES|ANNOTATE_VCF|FILTER_BY_CRIT|SNV_RELIABILITY_PIPE|DBSNP_COUNTER|FLAG_BIAS|CONFIDENCE_ANNOTATION' {
+    withName: 'GREP_SAMPLENAME|ANNOVAR|MUTATION_DISTANCE|CONTEXT_FREQUENCIES|ANNOTATE_VCF|FILTER_BY_CRIT|SNV_RELIABILITY_PIPE|DBSNP_COUNTER|FLAG_BIAS|CONFIDENCE_ANNOTATION|CONVERT_TO_VCF|FILE_CONCATENATOR' {
         publishDir = [
             path: { "${params.outdir}/test" },
             enabled: false