From a89cf5f891c6c86fad04cb3f8aafb7293ca4f1e8 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Tue, 26 Nov 2024 14:39:59 +0100
Subject: [PATCH 01/17] Improve fulltest

---
 conf/steps/imputation_glimpse1.config | 2 +-
 conf/steps/imputation_glimpse2.config | 2 +-
 conf/steps/simulation.config          | 1 +
 conf/steps/validation.config          | 1 +
 conf/test_full.config                 | 7 ++++---
 tests/csv/sample_sim_full_truth.csv   | 2 ++
 6 files changed, 10 insertions(+), 5 deletions(-)
 create mode 100644 tests/csv/sample_sim_full_truth.csv

diff --git a/conf/steps/imputation_glimpse1.config b/conf/steps/imputation_glimpse1.config
index d28ad992..7e31ce3d 100644
--- a/conf/steps/imputation_glimpse1.config
+++ b/conf/steps/imputation_glimpse1.config
@@ -61,7 +61,7 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_PHASE' {
         ext.args   = ["--impute-reference-only-variants"].join(' ')
         ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.glimpse1" }
-        ext.suffix = "bcf"
+        ext.suffix = "bcf.gz"
         publishDir = [ enabled: false ]
     }
 
diff --git a/conf/steps/imputation_glimpse2.config b/conf/steps/imputation_glimpse2.config
index 76ef02ce..bec0e5c9 100644
--- a/conf/steps/imputation_glimpse2.config
+++ b/conf/steps/imputation_glimpse2.config
@@ -21,7 +21,7 @@ process {
         cache = "lenient"
         ext.prefix   = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.glimpse2" }
         ext.args     = { "--keep-monomorphic-ref-sites" }
-        ext.suffix   = "bcf"
+        ext.suffix   = "bcf.gz"
         publishDir   = [ enabled: false ]
     }
 
diff --git a/conf/steps/simulation.config b/conf/steps/simulation.config
index 5b4ea805..71172319 100644
--- a/conf/steps/simulation.config
+++ b/conf/steps/simulation.config
@@ -17,6 +17,7 @@ process {
         tag = {"${meta.id} ${meta.chr}"}
     }
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_EXTRACT_REGION_SAMTOOLS:SAMTOOLS_VIEW' {
+        label = 'process_medium'
         ext.args   = ["--output-fmt bam", "--write-index"].join(' ')
         ext.prefix = { "${meta.id}_R${meta.region.replace(':','_')}" }
     }
diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index b5ca4fde..a95795b8 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -26,6 +26,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:BCFTOOLS_MPILEUP' {
+        label = 'process_high'
         ext.args = [
             "-I",
             "-E",
diff --git a/conf/test_full.config b/conf/test_full.config
index f4048ae4..61cfe3df 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -27,8 +27,9 @@ params {
     genome          = "GRCh38"
 
     // Input data
-    input  = "${projectDir}/tests/csv/sample_sim_full.csv"
-    panel  = "${projectDir}/tests/csv/panel_full.csv"
+    input       = "${projectDir}/tests/csv/sample_sim_full.csv"
+    input_truth = "${projectDir}/tests/csv/sample_sim_full_truth.csv"
+    panel       = "${projectDir}/tests/csv/panel_full.csv"
 
     // Pipeline steps
     steps  = "all"
@@ -40,5 +41,5 @@ params {
     phase          = false
 
     // Impute tools
-    tools = "glimpse1"
+    tools = "glimpse2"
 }
diff --git a/tests/csv/sample_sim_full_truth.csv b/tests/csv/sample_sim_full_truth.csv
new file mode 100644
index 00000000..2b089769
--- /dev/null
+++ b/tests/csv/sample_sim_full_truth.csv
@@ -0,0 +1,2 @@
+sample,file,index
+NA12878,ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz,ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.csi

From a9eafb3a1a5cf3747f07a4409eaa08012a1fdbf4 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Tue, 26 Nov 2024 14:45:10 +0100
Subject: [PATCH 02/17] Update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d147605d..afb17bd3 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -67,6 +67,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 - [#160](https://github.com/nf-core/phaseimpute/pull/160) - Improve `CHANGELOG.md` and add details to `usage.md`
 - [#158](https://github.com/nf-core/phaseimpute/pull/158) - Remove frequency computation and phasing from full test to reduce cost and computational time.
 - [#164](https://github.com/nf-core/phaseimpute/pull/164) - Rename `BAM_REGION_SAMTOOLS` to `BAM_EXTRACT_REGION_SAMTOOLS`. Remove `GLIMPSE2_SPLITREFERENCE` as it is not used. Add more steps to `test_all` profile for more exhaustivity.
+- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Improve configuration for demanding processes. Use Genome in a Bottle VCF benchmarking file for AWS full test.
 
 ### `Fixed`
 

From 79b7dfb517e9e9a1bfd5c501ed93f87a7efe9b57 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Tue, 26 Nov 2024 14:53:05 +0100
Subject: [PATCH 03/17] Revert extension change

---
 conf/steps/imputation_glimpse2.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/steps/imputation_glimpse2.config b/conf/steps/imputation_glimpse2.config
index bec0e5c9..76ef02ce 100644
--- a/conf/steps/imputation_glimpse2.config
+++ b/conf/steps/imputation_glimpse2.config
@@ -21,7 +21,7 @@ process {
         cache = "lenient"
         ext.prefix   = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.glimpse2" }
         ext.args     = { "--keep-monomorphic-ref-sites" }
-        ext.suffix   = "bcf.gz"
+        ext.suffix   = "bcf"
         publishDir   = [ enabled: false ]
     }
 

From 7a36d0447caed4bf127d49619f127e63ee2dc6ec Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Tue, 26 Nov 2024 14:54:14 +0100
Subject: [PATCH 04/17] Revert extension change

---
 conf/steps/imputation_glimpse1.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/conf/steps/imputation_glimpse1.config b/conf/steps/imputation_glimpse1.config
index 7e31ce3d..d28ad992 100644
--- a/conf/steps/imputation_glimpse1.config
+++ b/conf/steps/imputation_glimpse1.config
@@ -61,7 +61,7 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_IMPUTE_GLIMPSE1:GLIMPSE_PHASE' {
         ext.args   = ["--impute-reference-only-variants"].join(' ')
         ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chunk.replace(':','_')}.glimpse1" }
-        ext.suffix = "bcf.gz"
+        ext.suffix = "bcf"
         publishDir = [ enabled: false ]
     }
 

From 14d8aee023100f5e0d1529cdd502857670e00fe3 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Wed, 27 Nov 2024 17:56:38 +0100
Subject: [PATCH 05/17] Fix multiqc file names

---
 conf/modules.config                           | 29 ++++++++-
 conf/steps/panel_prep.config                  | 27 ++++++--
 conf/steps/simulation.config                  |  3 +
 conf/steps/validation.config                  | 21 ++++++-
 modules/nf-core/gawk/main.nf                  | 10 +--
 .../local/bam_extract_region_samtools/main.nf |  2 +-
 .../local/vcf_concordance_glimpse2/main.nf    | 18 +++++-
 workflows/phaseimpute/main.nf                 | 63 ++++++++++++++-----
 8 files changed, 142 insertions(+), 31 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 74062fa8..0e75eb81 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -32,11 +32,22 @@ process {
     // Coverage process
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_INP' {
         cache = "lenient"
-        ext.prefix = { "${meta.id}.truth" }
+        ext.prefix = { "${meta.id}.truth.allchr" }
         publishDir = [ enabled: false ]
     }
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SAMTOOLS_COVERAGE_DWN' {
         cache = "lenient"
+        ext.prefix = { "${meta.id}.allchr" }
+        publishDir = [ enabled: false ]
+    }
+
+    // Filter chromosomes in coverage
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:FILTER_CHR_INP' {
+        ext.prefix = { "${meta.id}.truth" }
+        publishDir = [ enabled: false ]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:FILTER_CHR_DWN' {
         ext.prefix = { "${meta.id}" }
         publishDir = [ enabled: false ]
     }
@@ -86,8 +97,22 @@ process {
         ]
     }
 
+    // Compute sample files for renaming
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BCFTOOLS_QUERY_IMPUTED' {
+        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
+        ext.args = '--list-samples'
+        publishDir = [enabled: false]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GAWK_IMPUTED' {
+        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
+        ext.prefix = { "${meta.id}_samples"}
+        ext.args2  = { "-v tools=\"${meta.tools}\" " + "'BEGIN { OFS = \"\\t\" } { print \$1, \"-\", \$1\".\"tools }'" }
+        publishDir = [enabled: false]
+    }
+
     // Split by samples for each tool
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_SPLIT_BCFTOOLS:BCFTOOLS_PLUGINSPLIT' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:SPLIT_IMPUTED:BCFTOOLS_PLUGINSPLIT' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.args   = ["--output-type z", "--write-index=tbi"].join(' ')
         publishDir = [
diff --git a/conf/steps/panel_prep.config b/conf/steps/panel_prep.config
index bd68b78e..99efa33b 100644
--- a/conf/steps/panel_prep.config
+++ b/conf/steps/panel_prep.config
@@ -56,8 +56,13 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: { !params.compute_freq && !params.phase }
+            saveAs: {
+                if ( !params.compute_freq && !params.phase ) {
+                    filename -> filename.equals('versions.yml') ? null : filename
+                } else {
+                    null
+                }
+            }
         ]
     }
 
@@ -66,8 +71,13 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: { !params.phase }
+            saveAs: {
+                if ( !params.phase ) {
+                    filename -> filename.equals('versions.yml') ? null : filename
+                } else {
+                    null
+                }
+            }
         ]
     }
 
@@ -76,8 +86,13 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-            enabled: { !params.phase }
+            saveAs: {
+                if ( !params.phase ) {
+                    filename -> filename.equals('versions.yml') ? null : filename
+                } else {
+                    null
+                }
+            }
         ]
     }
 
diff --git a/conf/steps/simulation.config b/conf/steps/simulation.config
index 71172319..17035abb 100644
--- a/conf/steps/simulation.config
+++ b/conf/steps/simulation.config
@@ -23,6 +23,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_EXTRACT_REGION_SAMTOOLS:SAMTOOLS_MERGE' {
+        cache = "lenient"
         ext.prefix = { "${meta.id}" }
         tag = {"${meta.id} ${meta.chr}"}
     }
@@ -34,6 +35,7 @@ process {
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE_SAMTOOLS:.*' {
         tag = {"${meta.id} ${meta.chr}"}
     }
+
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE_SAMTOOLS:SAMTOOLS_DEPTH' {
         publishDir = [enabled: false]
         ext.prefix = { "${meta1.id}_C${meta1.chr ?: "all"}.depth" }
@@ -49,6 +51,7 @@ process {
     }
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_DOWNSAMPLE_SAMTOOLS:SAMTOOLS_VIEW' {
+        cache = "lenient"
         ext.args   = ["--output-fmt bam", "--write-index"].join(' ')
         ext.prefix = { "${meta.id}.depth_${meta.depth}x" }
         publishDir = [
diff --git a/conf/steps/validation.config b/conf/steps/validation.config
index a95795b8..58103506 100644
--- a/conf/steps/validation.config
+++ b/conf/steps/validation.config
@@ -27,6 +27,7 @@ process {
 
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GL_TRUTH:BCFTOOLS_MPILEUP' {
         label = 'process_high'
+        cache = "lenient"
         ext.args = [
             "-I",
             "-E",
@@ -66,13 +67,13 @@ process {
     }
 
     // Compute sample files for renaming
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BCFTOOLS_QUERY' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BCFTOOLS_QUERY_TRUTH' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.args = '--list-samples'
         publishDir = [enabled: false]
     }
 
-    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GAWK' {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:GAWK_TRUTH' {
         tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
         ext.prefix = { "${meta.id}_samples"}
         ext.args2 = "'BEGIN { OFS = \"\\t\" } { print \$1, \"-\", \$1\".truth\" }'"
@@ -104,6 +105,22 @@ process {
         publishDir = [ enabled: false ]
     }
 
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GAWK_ERROR_SPL' {
+        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
+        ext.prefix = { "${meta.id}${meta.panel ? '_P' + meta.panel : ''}${meta.tools ? '_T' + meta.tools : ''}.concordance.renamed.error.spl" }
+        ext.suffix = "txt.gz"
+        ext.args2  = { "-v tool=\"${meta.tools}\" " + "'BEGIN { OFS = \" \" } !/^#/ { \$3 = \$3\".\"tool } { print }'" }
+        publishDir = [enabled: false]
+    }
+
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GAWK_RSQUARE_SPL' {
+        tag = { "${meta.id} Batch ${meta.batch} ${meta.tools}" }
+        ext.prefix = { "${meta.id}${meta.panel ? '_P' + meta.panel : ''}${meta.tools ? '_T' + meta.tools : ''}.concordance.renamed.rsquare.spl" }
+        ext.suffix = "txt.gz"
+        ext.args2  = { "-v tool=\"${meta.tools}\" " + "'BEGIN { OFS = \" \" } !/^#/ { \$1 = \$1\".\"tool } { print }'" }
+        publishDir = [enabled: false]
+    }
+
     withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GUNZIP' {
         ext.prefix = { "${meta.id}${meta.panel ? '_P' + meta.panel : ''}${meta.tools ? '_T' + meta.tools : ''}" }
         publishDir = [ enabled: false ]
diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf
index 7514246e..dca68b69 100644
--- a/modules/nf-core/gawk/main.nf
+++ b/modules/nf-core/gawk/main.nf
@@ -24,10 +24,11 @@ process GAWK {
     prefix = task.ext.prefix ?: "${meta.id}"
     suffix = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files
 
-    program   = program_file ? "-f ${program_file}" : "${args2}"
-    lst_gz    = input.collect{ it.getExtension().endsWith("gz") }
-    unzip     = lst_gz.contains(false) ? "" : "find ${input} -exec zcat {} \\; | \\"
-    input_cmd = unzip ? "" : "${input}"
+    program    = program_file ? "-f ${program_file}" : "${args2}"
+    lst_gz     = input.collect{ it.getExtension().endsWith("gz") }
+    unzip      = lst_gz.contains(false) ? "" : "find ${input} -exec zcat {} \\; | \\"
+    input_cmd  = unzip ? "" : "${input}"
+    output_cmd = suffix.endsWith("gz") ? "| gzip" : ""
 
     """
     ${unzip}
@@ -35,6 +36,7 @@ process GAWK {
         ${args} \\
         ${program} \\
         ${input_cmd} \\
+        ${output_cmd} \\
         > ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/subworkflows/local/bam_extract_region_samtools/main.nf b/subworkflows/local/bam_extract_region_samtools/main.nf
index 42f6a218..a8248ef8 100644
--- a/subworkflows/local/bam_extract_region_samtools/main.nf
+++ b/subworkflows/local/bam_extract_region_samtools/main.nf
@@ -35,7 +35,7 @@ workflow BAM_EXTRACT_REGION_SAMTOOLS {
             .map{
                 metaICR, bam, index -> [metaICR.subMap("id", "batch") + [chr: "all"], bam, index]
             }
-            .groupTuple(),
+            .groupTuple(sort: true),
         ch_fasta
     )
     ch_versions = ch_versions.mix(SAMTOOLS_MERGE.out.versions.first())
diff --git a/subworkflows/local/vcf_concordance_glimpse2/main.nf b/subworkflows/local/vcf_concordance_glimpse2/main.nf
index 82ba6592..ec4b04a0 100644
--- a/subworkflows/local/vcf_concordance_glimpse2/main.nf
+++ b/subworkflows/local/vcf_concordance_glimpse2/main.nf
@@ -2,6 +2,8 @@ include { GLIMPSE2_CONCORDANCE        } from '../../../modules/nf-core/glimpse2/
 include { GAWK                        } from '../../../modules/nf-core/gawk'
 include { ADD_COLUMNS                 } from '../../../modules/local/add_columns'
 include { GUNZIP                      } from '../../../modules/nf-core/gunzip'
+include { GAWK as GAWK_ERROR_SPL      } from '../../../modules/nf-core/gawk'
+include { GAWK as GAWK_RSQUARE_SPL    } from '../../../modules/nf-core/gawk'
 
 workflow VCF_CONCORDANCE_GLIMPSE2 {
 
@@ -35,11 +37,23 @@ workflow VCF_CONCORDANCE_GLIMPSE2 {
     )
     ch_versions = ch_versions.mix(GLIMPSE2_CONCORDANCE.out.versions.first())
 
+    GAWK_ERROR_SPL(
+        GLIMPSE2_CONCORDANCE.out.errors_spl,
+        []
+    )
+    ch_versions = ch_versions.mix(GAWK_ERROR_SPL.out.versions.first())
+
+    GAWK_RSQUARE_SPL(
+        GLIMPSE2_CONCORDANCE.out.rsquare_spl,
+        []
+    )
+    ch_versions = ch_versions.mix(GAWK_ERROR_SPL.out.versions.first())
+
     ch_multiqc_files = ch_multiqc_files.mix(GLIMPSE2_CONCORDANCE.out.errors_cal.map{ _meta, txt -> [txt]})
     ch_multiqc_files = ch_multiqc_files.mix(GLIMPSE2_CONCORDANCE.out.errors_grp.map{ _meta, txt -> [txt]})
-    ch_multiqc_files = ch_multiqc_files.mix(GLIMPSE2_CONCORDANCE.out.errors_spl.map{ _meta, txt -> [txt]})
+    ch_multiqc_files = ch_multiqc_files.mix(GAWK_ERROR_SPL.out.output.map{ _meta, txt -> [txt]})
     ch_multiqc_files = ch_multiqc_files.mix(GLIMPSE2_CONCORDANCE.out.rsquare_grp.map{ _meta, txt -> [txt]})
-    ch_multiqc_files = ch_multiqc_files.mix(GLIMPSE2_CONCORDANCE.out.rsquare_spl.map{ _meta, txt -> [txt]})
+    ch_multiqc_files = ch_multiqc_files.mix(GAWK_RSQUARE_SPL.out.output.map{ _meta, txt -> [txt]})
     ch_multiqc_files = ch_multiqc_files.mix(GLIMPSE2_CONCORDANCE.out.rsquare_per_site.map{ _meta, txt -> [txt]})
 
     GUNZIP(GLIMPSE2_CONCORDANCE.out.errors_grp)
diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
index 8e91d7f8..dbd0ac04 100644
--- a/workflows/phaseimpute/main.nf
+++ b/workflows/phaseimpute/main.nf
@@ -25,6 +25,8 @@ include { BAM_EXTRACT_REGION_SAMTOOLS                } from '../../subworkflows/
 include { BAM_DOWNSAMPLE_SAMTOOLS                    } from '../../subworkflows/local/bam_downsample_samtools'
 include { SAMTOOLS_COVERAGE as SAMTOOLS_COVERAGE_INP } from '../../modules/nf-core/samtools/coverage'
 include { SAMTOOLS_COVERAGE as SAMTOOLS_COVERAGE_DWN } from '../../modules/nf-core/samtools/coverage'
+include { GAWK as FILTER_CHR_INP                     } from '../../modules/nf-core/gawk'
+include { GAWK as FILTER_CHR_DWN                     } from '../../modules/nf-core/gawk'
 
 // Panelprep subworkflows
 include { VCF_NORMALIZE_BCFTOOLS                     } from '../../subworkflows/local/vcf_normalize_bcftools'
@@ -36,7 +38,9 @@ include { BCFTOOLS_STATS as BCFTOOLS_STATS_PANEL     } from '../../modules/nf-co
 
 // Imputation
 include { LIST_TO_FILE                               } from '../../modules/local/list_to_file'
-include { VCF_SPLIT_BCFTOOLS                         } from '../../subworkflows/local/vcf_split_bcftools'
+include { BCFTOOLS_QUERY as BCFTOOLS_QUERY_IMPUTED   } from '../../modules/nf-core/bcftools/query'
+include { GAWK as GAWK_IMPUTED                       } from '../../modules/nf-core/gawk'
+include { VCF_SPLIT_BCFTOOLS as SPLIT_IMPUTED        } from '../../subworkflows/local/vcf_split_bcftools'
 
 // GLIMPSE1 subworkflows
 include { BAM_GL_BCFTOOLS as GL_GLIMPSE1             } from '../../subworkflows/local/bam_gl_bcftools'
@@ -61,8 +65,8 @@ include { BCFTOOLS_STATS as BCFTOOLS_STATS_TOOLS     } from '../../modules/nf-co
 
 // Concordance subworkflows
 include { BAM_GL_BCFTOOLS as GL_TRUTH                } from '../../subworkflows/local/bam_gl_bcftools'
-include { BCFTOOLS_QUERY                             } from '../../modules/nf-core/bcftools/query'
-include { GAWK                                       } from '../../modules/nf-core/gawk'
+include { BCFTOOLS_QUERY as BCFTOOLS_QUERY_TRUTH     } from '../../modules/nf-core/bcftools/query'
+include { GAWK as GAWK_TRUTH                         } from '../../modules/nf-core/gawk'
 include { VCF_SPLIT_BCFTOOLS as SPLIT_TRUTH          } from '../../subworkflows/local/vcf_split_bcftools'
 include { BCFTOOLS_STATS as BCFTOOLS_STATS_TRUTH     } from '../../modules/nf-core/bcftools/stats'
 include { VCF_CONCATENATE_BCFTOOLS as CONCAT_TRUTH   } from '../../subworkflows/local/vcf_concatenate_bcftools'
@@ -116,10 +120,28 @@ workflow PHASEIMPUTE {
         // Use input for simulation as truth for validation step
         ch_input_truth = ch_input_sim
 
+        // Program to filter chromosomes
+        filter_chr_program = ch_region
+            .collect{ meta, region -> meta.chr }
+            .map { chr ->
+                "BEGIN { FS=\"\t\";\nsplit(\"" + chr.join(" ") + '", chr, " ");\n' +
+                'for (i in chr) {\nchr_map[chr[i]] = 1;\n}\n}\n' +
+                'NR == 1 || (\$1 in chr_map){\nprint \$0;\n}'
+            }
+            .collectFile(name:"program.txt")
+            .collect()
+
         // Compute coverage of input files
         SAMTOOLS_COVERAGE_INP(ch_input_sim, ch_fasta)
-        ch_versions      = ch_versions.mix(SAMTOOLS_COVERAGE_INP.out.versions)
-        ch_multiqc_files = ch_multiqc_files.mix(SAMTOOLS_COVERAGE_INP.out.coverage.map{it[1]})
+        ch_versions = ch_versions.mix(SAMTOOLS_COVERAGE_INP.out.versions)
+        ch_coverage = SAMTOOLS_COVERAGE_INP.out.coverage
+
+        FILTER_CHR_INP(
+            SAMTOOLS_COVERAGE_INP.out.coverage,
+            filter_chr_program
+        )
+        ch_versions = ch_versions.mix(FILTER_CHR_INP.out.versions)
+        ch_multiqc_files = ch_multiqc_files.mix(FILTER_CHR_INP.out.output.map{ it[1] })
 
         if (params.depth) {
             // Downsample input to desired depth
@@ -129,10 +151,17 @@ workflow PHASEIMPUTE {
 
             // Compute coverage of input files
             SAMTOOLS_COVERAGE_DWN(BAM_DOWNSAMPLE_SAMTOOLS.out.bam_emul, ch_fasta)
-            ch_versions      = ch_versions.mix(SAMTOOLS_COVERAGE_DWN.out.versions)
-            ch_multiqc_files = ch_multiqc_files.mix(SAMTOOLS_COVERAGE_DWN.out.coverage.map{it[1]})
-        }
+            ch_versions = ch_versions.mix(SAMTOOLS_COVERAGE_DWN.out.versions)
 
+            FILTER_CHR_DWN(
+                SAMTOOLS_COVERAGE_DWN.out.coverage,
+                filter_chr_program
+            )
+            ch_versions = ch_versions.mix(FILTER_CHR_DWN.out.versions)
+            ch_multiqc_files = ch_multiqc_files.mix(FILTER_CHR_DWN.out.output.map{ it[1] })
+        }
+        
+        
         if (params.genotype) {
             error "Genotype simulation not yet implemented"
         }
@@ -369,9 +398,15 @@ workflow PHASEIMPUTE {
             ch_input_validate = ch_input_validate.mix(CONCAT_QUILT.out.vcf_tbi)
         }
 
+        // Prepare renaming file
+        BCFTOOLS_QUERY_IMPUTED(ch_input_validate, [], [], [])
+        GAWK_IMPUTED(BCFTOOLS_QUERY_IMPUTED.out.output, [])
+        ch_split_imputed = ch_input_validate.join(GAWK_IMPUTED.out.output)
+
         // Split result by samples
-        VCF_SPLIT_BCFTOOLS(ch_input_validate.map{ [it[0], it[1], it[2], []] })
-        ch_input_validate = VCF_SPLIT_BCFTOOLS.out.vcf_tbi
+        SPLIT_IMPUTED(ch_split_imputed)
+        ch_versions = ch_versions.mix(SPLIT_IMPUTED.out.versions)
+        ch_input_validate = SPLIT_IMPUTED.out.vcf_tbi
 
         // Compute stats on imputed files
         BCFTOOLS_STATS_TOOLS(
@@ -442,12 +477,12 @@ workflow PHASEIMPUTE {
         ch_versions = ch_versions.mix(CONCAT_TRUTH.out.versions)
 
         // Prepare renaming file
-        BCFTOOLS_QUERY(CONCAT_TRUTH.out.vcf_tbi, [], [], [])
-        GAWK(BCFTOOLS_QUERY.out.output, [])
-        ch_pluginsplit = CONCAT_TRUTH.out.vcf_tbi.join(GAWK.out.output.view())
+        BCFTOOLS_QUERY_TRUTH(CONCAT_TRUTH.out.vcf_tbi, [], [], [])
+        GAWK_TRUTH(BCFTOOLS_QUERY_TRUTH.out.output, [])
+        ch_split_truth = CONCAT_TRUTH.out.vcf_tbi.join(GAWK_TRUTH.out.output)
 
         // Split truth vcf by samples
-        SPLIT_TRUTH(ch_pluginsplit)
+        SPLIT_TRUTH(ch_split_truth)
         ch_versions = ch_versions.mix(SPLIT_TRUTH.out.versions)
 
         // Compute stats on truth files

From 298296bf53369fc69d81be25d3b8965ef49178d9 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Wed, 27 Nov 2024 17:58:26 +0100
Subject: [PATCH 06/17] Update CHANGELOG

---
 CHANGELOG.md                  | 1 +
 workflows/phaseimpute/main.nf | 3 +--
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index afb17bd3..8078f3cc 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -81,6 +81,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
 - [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
 - [#162](https://github.com/nf-core/phaseimpute/pull/162) - Fix `fai` usage when provided by `genomes` parameter.
+- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Fix MULTIQC samples names. Fix output panel `publisDir`.
 - [#164](https://github.com/nf-core/phaseimpute/pull/164) - Improve documentation writing
 
 ### `Dependencies`
diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
index dbd0ac04..1e914b56 100644
--- a/workflows/phaseimpute/main.nf
+++ b/workflows/phaseimpute/main.nf
@@ -160,8 +160,7 @@ workflow PHASEIMPUTE {
             ch_versions = ch_versions.mix(FILTER_CHR_DWN.out.versions)
             ch_multiqc_files = ch_multiqc_files.mix(FILTER_CHR_DWN.out.output.map{ it[1] })
         }
-        
-        
+
         if (params.genotype) {
             error "Genotype simulation not yet implemented"
         }

From 21656bb9b852098b49308f0b2d7ab460fd56db97 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Wed, 27 Nov 2024 18:48:47 +0100
Subject: [PATCH 07/17] Update snapshot

---
 workflows/phaseimpute/tests/main.nf.test.snap | 146 +++++++++---------
 1 file changed, 73 insertions(+), 73 deletions(-)

diff --git a/workflows/phaseimpute/tests/main.nf.test.snap b/workflows/phaseimpute/tests/main.nf.test.snap
index 8553f530..43ece590 100644
--- a/workflows/phaseimpute/tests/main.nf.test.snap
+++ b/workflows/phaseimpute/tests/main.nf.test.snap
@@ -10,12 +10,12 @@
                 "imputation/stats/NA20359.stitch.bcftools_stats.txt",
                 "imputation/stitch/concat/all.batch0.stitch.vcf.gz",
                 "imputation/stitch/concat/all.batch0.stitch.vcf.gz.tbi",
-                "imputation/stitch/samples/NA12878.vcf.gz",
-                "imputation/stitch/samples/NA12878.vcf.gz.tbi",
-                "imputation/stitch/samples/NA19401.vcf.gz",
-                "imputation/stitch/samples/NA19401.vcf.gz.tbi",
-                "imputation/stitch/samples/NA20359.vcf.gz",
-                "imputation/stitch/samples/NA20359.vcf.gz.tbi"
+                "imputation/stitch/samples/NA12878.stitch.vcf.gz",
+                "imputation/stitch/samples/NA12878.stitch.vcf.gz.tbi",
+                "imputation/stitch/samples/NA19401.stitch.vcf.gz",
+                "imputation/stitch/samples/NA19401.stitch.vcf.gz.tbi",
+                "imputation/stitch/samples/NA20359.stitch.vcf.gz",
+                "imputation/stitch/samples/NA20359.stitch.vcf.gz.tbi"
             ],
             "VcfFile [chromosomes=[chr21, chr22], sampleCount=3, variantCount=1739, phased=false]",
             [
@@ -28,7 +28,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-22T13:07:42.012993182"
+        "timestamp": "2024-11-27T18:17:15.103980096"
     },
     "Check test_all": {
         "content": [
@@ -47,28 +47,28 @@
                 "imputation/csv/impute.csv",
                 "imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz",
                 "imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz.tbi",
-                "imputation/glimpse1/samples/NA12878.vcf.gz",
-                "imputation/glimpse1/samples/NA12878.vcf.gz.tbi",
-                "imputation/glimpse1/samples/NA19401.vcf.gz",
-                "imputation/glimpse1/samples/NA19401.vcf.gz.tbi",
-                "imputation/glimpse1/samples/NA20359.vcf.gz",
-                "imputation/glimpse1/samples/NA20359.vcf.gz.tbi",
+                "imputation/glimpse1/samples/NA12878.glimpse1.vcf.gz",
+                "imputation/glimpse1/samples/NA12878.glimpse1.vcf.gz.tbi",
+                "imputation/glimpse1/samples/NA19401.glimpse1.vcf.gz",
+                "imputation/glimpse1/samples/NA19401.glimpse1.vcf.gz.tbi",
+                "imputation/glimpse1/samples/NA20359.glimpse1.vcf.gz",
+                "imputation/glimpse1/samples/NA20359.glimpse1.vcf.gz.tbi",
                 "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz",
                 "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA12878.vcf.gz",
-                "imputation/glimpse2/samples/NA12878.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA19401.vcf.gz",
-                "imputation/glimpse2/samples/NA19401.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA20359.vcf.gz",
-                "imputation/glimpse2/samples/NA20359.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA12878.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA12878.glimpse2.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA19401.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA19401.glimpse2.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA20359.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA20359.glimpse2.vcf.gz.tbi",
                 "imputation/quilt/concat/all.batch0.quilt.vcf.gz",
                 "imputation/quilt/concat/all.batch0.quilt.vcf.gz.tbi",
-                "imputation/quilt/samples/NA12878.vcf.gz",
-                "imputation/quilt/samples/NA12878.vcf.gz.tbi",
-                "imputation/quilt/samples/NA19401.vcf.gz",
-                "imputation/quilt/samples/NA19401.vcf.gz.tbi",
-                "imputation/quilt/samples/NA20359.vcf.gz",
-                "imputation/quilt/samples/NA20359.vcf.gz.tbi",
+                "imputation/quilt/samples/NA12878.quilt.vcf.gz",
+                "imputation/quilt/samples/NA12878.quilt.vcf.gz.tbi",
+                "imputation/quilt/samples/NA19401.quilt.vcf.gz",
+                "imputation/quilt/samples/NA19401.quilt.vcf.gz.tbi",
+                "imputation/quilt/samples/NA20359.quilt.vcf.gz",
+                "imputation/quilt/samples/NA20359.quilt.vcf.gz.tbi",
                 "imputation/stats/NA12878.glimpse1.bcftools_stats.txt",
                 "imputation/stats/NA12878.glimpse2.bcftools_stats.txt",
                 "imputation/stats/NA12878.quilt.bcftools_stats.txt",
@@ -83,12 +83,12 @@
                 "imputation/stats/NA20359.stitch.bcftools_stats.txt",
                 "imputation/stitch/concat/all.batch0.stitch.vcf.gz",
                 "imputation/stitch/concat/all.batch0.stitch.vcf.gz.tbi",
-                "imputation/stitch/samples/NA12878.vcf.gz",
-                "imputation/stitch/samples/NA12878.vcf.gz.tbi",
-                "imputation/stitch/samples/NA19401.vcf.gz",
-                "imputation/stitch/samples/NA19401.vcf.gz.tbi",
-                "imputation/stitch/samples/NA20359.vcf.gz",
-                "imputation/stitch/samples/NA20359.vcf.gz.tbi"
+                "imputation/stitch/samples/NA12878.stitch.vcf.gz",
+                "imputation/stitch/samples/NA12878.stitch.vcf.gz.tbi",
+                "imputation/stitch/samples/NA19401.stitch.vcf.gz",
+                "imputation/stitch/samples/NA19401.stitch.vcf.gz.tbi",
+                "imputation/stitch/samples/NA20359.stitch.vcf.gz",
+                "imputation/stitch/samples/NA20359.stitch.vcf.gz.tbi"
             ],
             [
                 "prep_panel/chunks/glimpse1/1000GP_chr21_chunks_glimpse1.txt",
@@ -169,7 +169,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-22T13:58:54.188813202"
+        "timestamp": "2024-11-27T18:23:38.85114929"
     },
     "Check test_validate": {
         "content": [
@@ -207,22 +207,22 @@
                 "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz.tbi",
                 "imputation/glimpse2/concat/all.batch1.glimpse2.vcf.gz",
                 "imputation/glimpse2/concat/all.batch1.glimpse2.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA12878.vcf.gz",
-                "imputation/glimpse2/samples/NA12878.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA19401.vcf.gz",
-                "imputation/glimpse2/samples/NA19401.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA20359.vcf.gz",
-                "imputation/glimpse2/samples/NA20359.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA12878.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA12878.glimpse2.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA19401.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA19401.glimpse2.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA20359.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA20359.glimpse2.vcf.gz.tbi",
                 "imputation/quilt/concat/all.batch0.quilt.vcf.gz",
                 "imputation/quilt/concat/all.batch0.quilt.vcf.gz.tbi",
                 "imputation/quilt/concat/all.batch1.quilt.vcf.gz",
                 "imputation/quilt/concat/all.batch1.quilt.vcf.gz.tbi",
-                "imputation/quilt/samples/NA12878.vcf.gz",
-                "imputation/quilt/samples/NA12878.vcf.gz.tbi",
-                "imputation/quilt/samples/NA19401.vcf.gz",
-                "imputation/quilt/samples/NA19401.vcf.gz.tbi",
-                "imputation/quilt/samples/NA20359.vcf.gz",
-                "imputation/quilt/samples/NA20359.vcf.gz.tbi",
+                "imputation/quilt/samples/NA12878.quilt.vcf.gz",
+                "imputation/quilt/samples/NA12878.quilt.vcf.gz.tbi",
+                "imputation/quilt/samples/NA19401.quilt.vcf.gz",
+                "imputation/quilt/samples/NA19401.quilt.vcf.gz.tbi",
+                "imputation/quilt/samples/NA20359.quilt.vcf.gz",
+                "imputation/quilt/samples/NA20359.quilt.vcf.gz.tbi",
                 "imputation/stats/NA12878.glimpse2.bcftools_stats.txt",
                 "imputation/stats/NA12878.quilt.bcftools_stats.txt",
                 "imputation/stats/NA19401.glimpse2.bcftools_stats.txt",
@@ -271,7 +271,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-22T14:06:57.642618122"
+        "timestamp": "2024-11-27T18:30:51.51345352"
     },
     "Check test_quilt": {
         "content": [
@@ -281,12 +281,12 @@
                 "imputation/csv/impute.csv",
                 "imputation/quilt/concat/all.batch0.quilt.vcf.gz",
                 "imputation/quilt/concat/all.batch0.quilt.vcf.gz.tbi",
-                "imputation/quilt/samples/NA12878.vcf.gz",
-                "imputation/quilt/samples/NA12878.vcf.gz.tbi",
-                "imputation/quilt/samples/NA19401.vcf.gz",
-                "imputation/quilt/samples/NA19401.vcf.gz.tbi",
-                "imputation/quilt/samples/NA20359.vcf.gz",
-                "imputation/quilt/samples/NA20359.vcf.gz.tbi",
+                "imputation/quilt/samples/NA12878.quilt.vcf.gz",
+                "imputation/quilt/samples/NA12878.quilt.vcf.gz.tbi",
+                "imputation/quilt/samples/NA19401.quilt.vcf.gz",
+                "imputation/quilt/samples/NA19401.quilt.vcf.gz.tbi",
+                "imputation/quilt/samples/NA20359.quilt.vcf.gz",
+                "imputation/quilt/samples/NA20359.quilt.vcf.gz.tbi",
                 "imputation/stats/NA12878.quilt.bcftools_stats.txt",
                 "imputation/stats/NA19401.quilt.bcftools_stats.txt",
                 "imputation/stats/NA20359.quilt.bcftools_stats.txt"
@@ -302,7 +302,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-23T19:41:54.261988901"
+        "timestamp": "2024-11-27T18:15:27.194211063"
     },
     "Check test_sim": {
         "content": [
@@ -362,12 +362,12 @@
                 "imputation/csv/impute.csv",
                 "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz",
                 "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA12878.vcf.gz",
-                "imputation/glimpse2/samples/NA12878.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA19401.vcf.gz",
-                "imputation/glimpse2/samples/NA19401.vcf.gz.tbi",
-                "imputation/glimpse2/samples/NA20359.vcf.gz",
-                "imputation/glimpse2/samples/NA20359.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA12878.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA12878.glimpse2.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA19401.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA19401.glimpse2.vcf.gz.tbi",
+                "imputation/glimpse2/samples/NA20359.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/NA20359.glimpse2.vcf.gz.tbi",
                 "imputation/stats/NA12878.glimpse2.bcftools_stats.txt",
                 "imputation/stats/NA19401.glimpse2.bcftools_stats.txt",
                 "imputation/stats/NA20359.glimpse2.bcftools_stats.txt"
@@ -383,7 +383,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-22T13:03:28.516026252"
+        "timestamp": "2024-11-27T18:13:04.376764506"
     },
     "Check test": {
         "content": [
@@ -393,12 +393,12 @@
                 "imputation/csv/impute.csv",
                 "imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz",
                 "imputation/glimpse1/concat/all.batch0.glimpse1.vcf.gz.tbi",
-                "imputation/glimpse1/samples/NA12878.vcf.gz",
-                "imputation/glimpse1/samples/NA12878.vcf.gz.tbi",
-                "imputation/glimpse1/samples/NA19401.vcf.gz",
-                "imputation/glimpse1/samples/NA19401.vcf.gz.tbi",
-                "imputation/glimpse1/samples/NA20359.vcf.gz",
-                "imputation/glimpse1/samples/NA20359.vcf.gz.tbi",
+                "imputation/glimpse1/samples/NA12878.glimpse1.vcf.gz",
+                "imputation/glimpse1/samples/NA12878.glimpse1.vcf.gz.tbi",
+                "imputation/glimpse1/samples/NA19401.glimpse1.vcf.gz",
+                "imputation/glimpse1/samples/NA19401.glimpse1.vcf.gz.tbi",
+                "imputation/glimpse1/samples/NA20359.glimpse1.vcf.gz",
+                "imputation/glimpse1/samples/NA20359.glimpse1.vcf.gz.tbi",
                 "imputation/stats/NA12878.glimpse1.bcftools_stats.txt",
                 "imputation/stats/NA19401.glimpse1.bcftools_stats.txt",
                 "imputation/stats/NA20359.glimpse1.bcftools_stats.txt"
@@ -414,7 +414,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-23T19:36:03.277999895"
+        "timestamp": "2024-11-27T18:11:44.567996758"
     },
     "Check test_dog": {
         "content": [
@@ -447,16 +447,16 @@
                 "imputation/csv/impute.csv",
                 "imputation/glimpse1/concat/dog_1735.batch0.glimpse1.vcf.gz",
                 "imputation/glimpse1/concat/dog_1735.batch0.glimpse1.vcf.gz.tbi",
-                "imputation/glimpse1/samples/dog_1735.vcf.gz",
-                "imputation/glimpse1/samples/dog_1735.vcf.gz.tbi",
+                "imputation/glimpse1/samples/dog_1735.glimpse1.vcf.gz",
+                "imputation/glimpse1/samples/dog_1735.glimpse1.vcf.gz.tbi",
                 "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz",
                 "imputation/glimpse2/concat/all.batch0.glimpse2.vcf.gz.tbi",
-                "imputation/glimpse2/samples/dog_1735.vcf.gz",
-                "imputation/glimpse2/samples/dog_1735.vcf.gz.tbi",
+                "imputation/glimpse2/samples/dog_1735.glimpse2.vcf.gz",
+                "imputation/glimpse2/samples/dog_1735.glimpse2.vcf.gz.tbi",
                 "imputation/quilt/concat/all.batch0.quilt.vcf.gz",
                 "imputation/quilt/concat/all.batch0.quilt.vcf.gz.tbi",
-                "imputation/quilt/samples/1735.vcf.gz",
-                "imputation/quilt/samples/1735.vcf.gz.tbi",
+                "imputation/quilt/samples/1735.quilt.vcf.gz",
+                "imputation/quilt/samples/1735.quilt.vcf.gz.tbi",
                 "imputation/stats/1735.quilt.bcftools_stats.txt",
                 "imputation/stats/dog_1735.glimpse1.bcftools_stats.txt",
                 "imputation/stats/dog_1735.glimpse2.bcftools_stats.txt"
@@ -466,6 +466,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-22T13:16:12.803136748"
+        "timestamp": "2024-11-27T18:25:56.980470563"
     }
 }
\ No newline at end of file

From 8d97f749c0df657215e3d139258eb45583332470 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Thu, 28 Nov 2024 16:12:40 +0100
Subject: [PATCH 08/17] Update gawk

---
 modules.json                                  |  5 +-
 modules/nf-core/gawk/main.nf                  | 12 ++-
 modules/nf-core/gawk/tests/main.nf.test       | 77 +++++++++++++++++--
 modules/nf-core/gawk/tests/main.nf.test.snap  | 35 ++++++++-
 modules/nf-core/gawk/tests/nextflow.config    |  4 +-
 .../tests/nextflow_with_program_file.config   |  5 --
 6 files changed, 115 insertions(+), 23 deletions(-)
 delete mode 100644 modules/nf-core/gawk/tests/nextflow_with_program_file.config

diff --git a/modules.json b/modules.json
index b40eb508..f3cd1cb6 100644
--- a/modules.json
+++ b/modules.json
@@ -72,9 +72,8 @@
                     },
                     "gawk": {
                         "branch": "master",
-                        "git_sha": "97321eded31a12598837a476d3615300af413bb7",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/gawk/gawk.diff"
+                        "git_sha": "caab1314ca62679b629da4c79afa9a4cab2bb8ee",
+                        "installed_by": ["modules"]
                     },
                     "glimpse/chunk": {
                         "branch": "master",
diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf
index dca68b69..b9df2b8c 100644
--- a/modules/nf-core/gawk/main.nf
+++ b/modules/nf-core/gawk/main.nf
@@ -24,12 +24,16 @@ process GAWK {
     prefix = task.ext.prefix ?: "${meta.id}"
     suffix = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files
 
-    program    = program_file ? "-f ${program_file}" : "${args2}"
-    lst_gz     = input.collect{ it.getExtension().endsWith("gz") }
-    unzip      = lst_gz.contains(false) ? "" : "find ${input} -exec zcat {} \\; | \\"
-    input_cmd  = unzip ? "" : "${input}"
+    program   = program_file ? "-f ${program_file}" : "${args2}"
+    lst_gz    = input.collect{ it.getExtension().endsWith("gz") }
+    unzip     = lst_gz.contains(false) ? "" : "find ${input} -exec zcat {} \\; | \\"
+    input_cmd = unzip ? "" : "${input}"
     output_cmd = suffix.endsWith("gz") ? "| gzip" : ""
 
+    input.collect{
+        assert it.name != "${prefix}.${suffix}" : "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    }
+
     """
     ${unzip}
     awk \\
diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test
index 5952e9a2..b3cde8bf 100644
--- a/modules/nf-core/gawk/tests/main.nf.test
+++ b/modules/nf-core/gawk/tests/main.nf.test
@@ -8,10 +8,14 @@ nextflow_process {
     tag "modules_nfcore"
     tag "gawk"
 
-    test("Convert fasta to bed") {
-        config "./nextflow.config"
+    config "./nextflow.config"
 
+    test("Convert fasta to bed") {
         when {
+            params {
+                gawk_suffix = "bed"
+                gawk_args2  = '\'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}\''
+            }
             process {
                 """
                 input[0] = [
@@ -32,9 +36,11 @@ nextflow_process {
     }
 
     test("Convert fasta to bed with program file") {
-        config "./nextflow_with_program_file.config"
-
         when {
+            params {
+                gawk_suffix = "bed"
+                gawk_args2  = ""
+            }
             process {
                 """
                 input[0] = [
@@ -55,9 +61,11 @@ nextflow_process {
     }
 
     test("Extract first column from multiple files") {
-        config "./nextflow_with_program_file.config"
-        tag "test"
         when {
+            params {
+                gawk_suffix = "bed"
+                gawk_args2  = ""
+            }
             process {
                 """
                 input[0] = [
@@ -79,9 +87,11 @@ nextflow_process {
     }
 
     test("Unzip files before processing") {
-        config "./nextflow_with_program_file.config"
-
         when {
+            params {
+                gawk_suffix = "bed"
+                gawk_args2  = ""
+            }
             process {
                 """
                 input[0] = [
@@ -101,4 +111,55 @@ nextflow_process {
             )
         }
     }
+
+    test("Compress after processing") {
+        when {
+            params {
+                gawk_suffix = "txt.gz"
+                gawk_args2  = '\'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}\''
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Input and output files are similar") {
+        when {
+            params {
+                gawk_suffix = "txt"
+                gawk_args2  = ""
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'hello' ], // meta map
+                    [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)]
+                ]
+                input[1] = Channel.of('BEGIN {FS=" "}; {print \$1}').collectFile(name:"program.txt")
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.failed },
+                { assert process.errorReport.contains("Input and output names are the same, set prefix in module configuration to disambiguate!") }
+            )
+        }
+    }
 }
\ No newline at end of file
diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap
index d396f738..1b3c2f71 100644
--- a/modules/nf-core/gawk/tests/main.nf.test.snap
+++ b/modules/nf-core/gawk/tests/main.nf.test.snap
@@ -1,4 +1,37 @@
 {
+    "Compress after processing": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt.gz:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-27T17:11:20.054143406"
+    },
     "Convert fasta to bed": {
         "content": [
             {
@@ -131,4 +164,4 @@
         },
         "timestamp": "2024-10-19T22:08:19.533527657"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/gawk/tests/nextflow.config b/modules/nf-core/gawk/tests/nextflow.config
index 6e5d43a3..895709a7 100644
--- a/modules/nf-core/gawk/tests/nextflow.config
+++ b/modules/nf-core/gawk/tests/nextflow.config
@@ -1,6 +1,6 @@
 process {
     withName: GAWK {
-        ext.suffix = "bed"
-        ext.args2 = '\'BEGIN {FS="\t"}; {print \$1 FS "0" FS \$2}\''
+        ext.suffix = params.gawk_suffix
+        ext.args2  = params.gawk_args2
     }
 }
diff --git a/modules/nf-core/gawk/tests/nextflow_with_program_file.config b/modules/nf-core/gawk/tests/nextflow_with_program_file.config
deleted file mode 100644
index 693ad419..00000000
--- a/modules/nf-core/gawk/tests/nextflow_with_program_file.config
+++ /dev/null
@@ -1,5 +0,0 @@
-process {
-    withName: GAWK {
-        ext.suffix = "bed"
-    }
-}

From 8e271b4cebd26424ec53c52a53169c7223cd3ec3 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 2 Dec 2024 09:32:04 +0100
Subject: [PATCH 09/17] Update CHANGELOG

---
 CHANGELOG.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8078f3cc..fb034907 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -67,7 +67,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 - [#160](https://github.com/nf-core/phaseimpute/pull/160) - Improve `CHANGELOG.md` and add details to `usage.md`
 - [#158](https://github.com/nf-core/phaseimpute/pull/158) - Remove frequency computation and phasing from full test to reduce cost and computational time.
 - [#164](https://github.com/nf-core/phaseimpute/pull/164) - Rename `BAM_REGION_SAMTOOLS` to `BAM_EXTRACT_REGION_SAMTOOLS`. Remove `GLIMPSE2_SPLITREFERENCE` as it is not used. Add more steps to `test_all` profile for more exhaustivity.
-- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Improve configuration for demanding processes. Use Genome in a Bottle VCF benchmarking file for AWS full test.
+- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Improve configuration for demanding processes. Use Genome in a Bottle VCF benchmarking file for AWS full test. Moved from `glimpse1` to `glimpse2` for the full test profile.
 
 ### `Fixed`
 
@@ -81,7 +81,7 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
 - [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
 - [#162](https://github.com/nf-core/phaseimpute/pull/162) - Fix `fai` usage when provided by `genomes` parameter.
-- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Fix MULTIQC samples names. Fix output panel `publisDir`.
+- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Fix MULTIQC samples names (add post-processing for clean up `FILTER_CHR_DWN`, `FILTER_CHR_INP`, `GAWK_ERROR_SPL`, `GAWK_RSQUARE_SPL`). Fix output panel `publisDir`.
 - [#164](https://github.com/nf-core/phaseimpute/pull/164) - Improve documentation writing
 
 ### `Dependencies`

From 1f6c784fd88a8fc58b9e0107bf8f22095fd29d95 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 2 Dec 2024 16:58:35 +0100
Subject: [PATCH 10/17] Fix configuration

---
 conf/steps/panel_prep.config | 12 ++++++------
 conf/test_full.config        | 12 ++++++++++++
 2 files changed, 18 insertions(+), 6 deletions(-)

diff --git a/conf/steps/panel_prep.config b/conf/steps/panel_prep.config
index 99efa33b..23675e9b 100644
--- a/conf/steps/panel_prep.config
+++ b/conf/steps/panel_prep.config
@@ -56,9 +56,9 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,
-            saveAs: {
+            saveAs: { filename ->
                 if ( !params.compute_freq && !params.phase ) {
-                    filename -> filename.equals('versions.yml') ? null : filename
+                    filename.equals('versions.yml') ? null : filename
                 } else {
                     null
                 }
@@ -71,9 +71,9 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,
-            saveAs: {
+            saveAs: { filename ->
                 if ( !params.phase ) {
-                    filename -> filename.equals('versions.yml') ? null : filename
+                    filename.equals('versions.yml') ? null : filename
                 } else {
                     null
                 }
@@ -86,9 +86,9 @@ process {
         publishDir = [
             path: { "${params.outdir}/prep_panel/panel" },
             mode: params.publish_dir_mode,
-            saveAs: {
+            saveAs: { filename ->
                 if ( !params.phase ) {
-                    filename -> filename.equals('versions.yml') ? null : filename
+                    filename.equals('versions.yml') ? null : filename
                 } else {
                     null
                 }
diff --git a/conf/test_full.config b/conf/test_full.config
index 61cfe3df..94e04dd9 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -42,4 +42,16 @@ params {
 
     // Impute tools
     tools = "glimpse2"
+
+    // Concordance arguments
+    min_val_gl = null
+    min_val_dp = null
+}
+
+process {
+    withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:VCF_CONCORDANCE_GLIMPSE2:GLIMPSE2_CONCORDANCE' {
+        ext.args = "--gt-val --af-tag AF"
+        ext.prefix = { "${meta.id}${meta.panel ? '_P' + meta.panel : ''}${meta.tools ? '_T' + meta.tools : ''}.concordance" }
+        publishDir = [ enabled: false ]
+    }
 }

From 98fbeaa736c15ddff40d5af58d9c748883c147fd Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 2 Dec 2024 17:00:30 +0100
Subject: [PATCH 11/17] Update sample samplesheet

---
 tests/csv/sample_sim_full.csv       | 2 +-
 tests/csv/sample_sim_full_truth.csv | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/csv/sample_sim_full.csv b/tests/csv/sample_sim_full.csv
index cc9f4828..5100bfa1 100644
--- a/tests/csv/sample_sim_full.csv
+++ b/tests/csv/sample_sim_full.csv
@@ -1,2 +1,2 @@
 sample,file,index
-NA12878,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239334/NA12878.final.cram,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239334/NA12878.final.cram.crai
+HG001,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239334/NA12878.final.cram,ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239334/NA12878.final.cram.crai
diff --git a/tests/csv/sample_sim_full_truth.csv b/tests/csv/sample_sim_full_truth.csv
index 2b089769..e65884d9 100644
--- a/tests/csv/sample_sim_full_truth.csv
+++ b/tests/csv/sample_sim_full_truth.csv
@@ -1,2 +1,2 @@
 sample,file,index
-NA12878,ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz,ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.csi
+HG001,https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz,https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi

From 275d31d994c77dc3e1fadeadd25103fc3036acb4 Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 2 Dec 2024 17:01:25 +0100
Subject: [PATCH 12/17] Fix input truth vcf usage

---
 main.nf                       | 7 -------
 workflows/phaseimpute/main.nf | 7 +++++--
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/main.nf b/main.nf
index 0c3f01ec..b31db4b1 100644
--- a/main.nf
+++ b/main.nf
@@ -80,13 +80,6 @@ workflow NFCORE_PHASEIMPUTE {
         ch_input_validate = ch_input
     }
 
-    if (params.steps.split(',').contains("all")) {
-        ch_input_truth.map{
-            error "Cannot run all steps with --input-truth"
-        }
-        ch_input_truth = ch_input
-    }
-
     //
     // WORKFLOW: Run pipeline
     //
diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
index 1e914b56..47724cc4 100644
--- a/workflows/phaseimpute/main.nf
+++ b/workflows/phaseimpute/main.nf
@@ -118,7 +118,10 @@ workflow PHASEIMPUTE {
         }
 
         // Use input for simulation as truth for validation step
-        ch_input_truth = ch_input_sim
+        // if no truth is provided
+        if (!params.input_truth) {
+            ch_input_truth = ch_input_sim
+        }
 
         // Program to filter chromosomes
         filter_chr_program = ch_region
@@ -491,7 +494,7 @@ workflow PHASEIMPUTE {
             [[],[]],
             [[],[]],
             [[],[]],
-            ch_fasta.map{ [it[0], it[1]] }
+            [[],[]] //ch_fasta.map{ [it[0], it[1]] }
         )
         ch_versions = ch_versions.mix(BCFTOOLS_STATS_TRUTH.out.versions)
         ch_multiqc_files = ch_multiqc_files.mix(BCFTOOLS_STATS_TRUTH.out.stats.map{ [it[1]] })

From 69306d93e1c63f444651aee39f9f55926d73fb1e Mon Sep 17 00:00:00 2001
From: Louis Le Nezet <louislenezet@gmail.com>
Date: Mon, 2 Dec 2024 17:01:54 +0100
Subject: [PATCH 13/17] Fix glimpse2 concordance usage

---
 modules/nf-core/glimpse2/concordance/main.nf  | 30 +++++++++++--------
 .../local/vcf_concordance_glimpse2/main.nf    |  3 +-
 2 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/modules/nf-core/glimpse2/concordance/main.nf b/modules/nf-core/glimpse2/concordance/main.nf
index 06eb139b..f96f5c38 100644
--- a/modules/nf-core/glimpse2/concordance/main.nf
+++ b/modules/nf-core/glimpse2/concordance/main.nf
@@ -9,9 +9,7 @@ process GLIMPSE2_CONCORDANCE {
 
     input:
     tuple val(meta), path(estimate), path(estimate_index), path(truth), path(truth_index), path(freq), path(freq_index), path(samples), val(region)
-    tuple val(meta2), path(groups), val(bins), val(ac_bins), val(allele_counts)
-    val(min_val_gl)
-    val(min_val_dp)
+    tuple val(meta2), path(groups), val(bins), val(ac_bins), val(allele_counts), val(min_val_gl), val(min_val_dp)
 
     output:
     tuple val(meta), path("*.error.cal.txt.gz")  , emit: errors_cal
@@ -26,17 +24,23 @@ process GLIMPSE2_CONCORDANCE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args         = task.ext.args          ?: ''
-    def prefix       = task.ext.prefix        ?: "${meta.id}"
-    def samples_cmd  = samples                ? "--samples ${samples}"             : ""
-    def groups_cmd   = groups                 ? "--groups ${groups}"               : ""
-    def bins_cmd     = bins                   ? "--bins ${bins}"                   : ""
-    def ac_bins_cmd  = ac_bins                ? "--ac-bins ${ac_bins}"             : ""
-    def ale_ct_cmd   = allele_counts          ? "--allele-counts ${allele_counts}" : ""
-    def region_str   = region instanceof List ? region.join('\\n')                 : region
+    def args           = task.ext.args          ?: ''
+    def prefix         = task.ext.prefix        ?: "${meta.id}"
+    def samples_cmd    = samples                ? "--samples ${samples}"             : ""
+    def groups_cmd     = groups                 ? "--groups ${groups}"               : ""
+    def bins_cmd       = bins                   ? "--bins ${bins}"                   : ""
+    def ac_bins_cmd    = ac_bins                ? "--ac-bins ${ac_bins}"             : ""
+    def ale_ct_cmd     = allele_counts          ? "--allele-counts ${allele_counts}" : ""
+    def min_val_gl_cmd = min_val_gl             ? "--min-val-gl ${min_val_gl}"       : ""
+    def min_val_dp_cmd = min_val_dp             ? "--min-val-dp ${min_val_dp}"       : ""
+    def region_str     = region instanceof List ? region.join('\\n')                 : region
 
     if (((groups ? 1:0) + (bins ? 1:0) + (ac_bins ? 1:0) + (allele_counts ? 1:0)) != 1) error "One and only one argument should be selected between groups, bins, ac_bins, allele_counts"
 
+    if (args.contains("--gt-val")) {
+        assert !(min_val_gl || min_val_dp) : "If --gt-val is set, --min-val-gl nor --min-val-dp must be set"
+    }
+
     """
     printf '$region_str' > regions.txt
     sed 's/\$/ $freq $truth $estimate/' regions.txt > input.txt
@@ -47,8 +51,8 @@ process GLIMPSE2_CONCORDANCE {
         $bins_cmd \\
         $ac_bins_cmd \\
         $ale_ct_cmd \\
-        --min-val-gl $min_val_gl \\
-        --min-val-dp $min_val_dp \\
+        $min_val_gl_cmd \\
+        $min_val_dp_cmd \\
         --input input.txt \\
         --thread $task.cpus \\
         --output ${prefix}
diff --git a/subworkflows/local/vcf_concordance_glimpse2/main.nf b/subworkflows/local/vcf_concordance_glimpse2/main.nf
index ec4b04a0..8545d6a0 100644
--- a/subworkflows/local/vcf_concordance_glimpse2/main.nf
+++ b/subworkflows/local/vcf_concordance_glimpse2/main.nf
@@ -32,8 +32,7 @@ workflow VCF_CONCORDANCE_GLIMPSE2 {
 
     GLIMPSE2_CONCORDANCE (
         ch_concordance,
-        [[], [], params.bins, [], []],
-        params.min_val_gl, params.min_val_dp
+        [[], [], params.bins, [], [], params.min_val_gl, params.min_val_dp]
     )
     ch_versions = ch_versions.mix(GLIMPSE2_CONCORDANCE.out.versions.first())
 

From 0d90bb25d8ad1c5666449c5daa747af3c29a6e3f Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Mon, 2 Dec 2024 19:09:32 +0100
Subject: [PATCH 14/17] Reverse modification

---
 workflows/phaseimpute/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/phaseimpute/main.nf b/workflows/phaseimpute/main.nf
index 47724cc4..111fc315 100644
--- a/workflows/phaseimpute/main.nf
+++ b/workflows/phaseimpute/main.nf
@@ -494,7 +494,7 @@ workflow PHASEIMPUTE {
             [[],[]],
             [[],[]],
             [[],[]],
-            [[],[]] //ch_fasta.map{ [it[0], it[1]] }
+            ch_fasta.map{ [it[0], it[1]] }
         )
         ch_versions = ch_versions.mix(BCFTOOLS_STATS_TRUTH.out.versions)
         ch_multiqc_files = ch_multiqc_files.mix(BCFTOOLS_STATS_TRUTH.out.stats.map{ [it[1]] })

From 9b630c3163b6352fc046560f326460fa6c243b9a Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Wed, 4 Dec 2024 11:26:02 +0100
Subject: [PATCH 15/17] Update glimpse2 concordance

---
 modules.json                                  |   2 +-
 modules/nf-core/glimpse2/concordance/meta.yml |   4 +-
 .../glimpse2/concordance/tests/main.nf.test   | 155 ++++--------------
 .../concordance/tests/main.nf.test.snap       |  45 +----
 .../concordance/tests/nextflow.config         |   4 +-
 .../concordance/tests/nextflow_R2.config      |   7 -
 6 files changed, 49 insertions(+), 168 deletions(-)
 delete mode 100644 modules/nf-core/glimpse2/concordance/tests/nextflow_R2.config

diff --git a/modules.json b/modules.json
index f3cd1cb6..25071320 100644
--- a/modules.json
+++ b/modules.json
@@ -98,7 +98,7 @@
                     },
                     "glimpse2/concordance": {
                         "branch": "master",
-                        "git_sha": "cc64e71652f67ce627064af51008fe0a00850987",
+                        "git_sha": "6aed50284f6b208fd8eff1ec1dae4b25bf03c432",
                         "installed_by": ["modules"]
                     },
                     "glimpse2/ligate": {
diff --git a/modules/nf-core/glimpse2/concordance/meta.yml b/modules/nf-core/glimpse2/concordance/meta.yml
index f286f6e9..a9e27c90 100644
--- a/modules/nf-core/glimpse2/concordance/meta.yml
+++ b/modules/nf-core/glimpse2/concordance/meta.yml
@@ -79,12 +79,12 @@ input:
         description: |
           Default allele count bins used for rsquared computations.
           AN field must be defined in the frequency file.
-  - - min_val_gl:
+    - min_val_gl:
         type: float
         description: |
           Minimum genotype likelihood probability P(G|R) in validation data.
           Set to zero to have no filter of if using –gt-validation
-  - - min_val_dp:
+    - min_val_dp:
         type: integer
         description: |
           Minimum coverage in validation data.
diff --git a/modules/nf-core/glimpse2/concordance/tests/main.nf.test b/modules/nf-core/glimpse2/concordance/tests/main.nf.test
index 9c562520..d1c68bc2 100644
--- a/modules/nf-core/glimpse2/concordance/tests/main.nf.test
+++ b/modules/nf-core/glimpse2/concordance/tests/main.nf.test
@@ -10,78 +10,36 @@ nextflow_process {
     tag "modules_nfcore"
     tag "modules"
 
-    setup {
-        run("GLIMPSE2_PHASE") {
-            script "../../phase/main.nf"
-            process {
-                """
-                input_vcf     = Channel.of([
-                    [ id:'input'], // meta map
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz", checkIfExists: true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.1x.vcf.gz.csi", checkIfExists: true),
-                    []
-                ])
-
-                samples_infos = Channel.of('NA12878 2').collectFile(name: 'sampleinfos.txt')
-                region        = Channel.of(["chr21:16600000-16800000","chr21:16650000-16750000"])
-
-                ch_ref_panel = Channel.of([
-                        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf", checkIfExists: true),
-                        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.bcf.csi", checkIfExists: true)
-                ])
-
-                ch_map = Channel.of([
-                        file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/chr21.b38.gmap.gz", checkIfExists: true),
-                ])
-
-                // [meta, vcf, index, sample_infos, regionin, regionout, regionindex, ref, ref_index, map]
-                input[0] =  input_vcf
-                    .combine(samples_infos)
-                    .combine(region)
-                    .combine( ch_ref_panel )
-                    .combine( ch_map )
-                input[1]= Channel.of([[],[],[]])
-                """
-            }
-        }
-
-        run("BCFTOOLS_INDEX") {
-            script "../../../bcftools/index/main.nf"
-            process {
-                """
-                input[0] = GLIMPSE2_PHASE.output.phased_variants
-                """
-            }
-        }
-    }
-
-
-    test("test_glimpse2_concordance") {
+    test("test glimpse2 concordance") {
         config "./nextflow.config"
 
         when {
+            params {
+                glimpse2_concordance_args = "--gt-val --af-tag AF"
+            }
             process {
                 """
-                allele_freq = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
+                target = Channel.of([
+                    [id: "input"],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi",checkIfExists:true)
                 ])
-
                 truth = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi",checkIfExists:true)
                 ])
-                list_inputs = GLIMPSE2_PHASE.output.phased_variants
-                        .join( BCFTOOLS_INDEX.out.csi )
+                allele_freq = Channel.of([
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz.csi",checkIfExists:true)
+                ])
+                list_inputs = target
                         .combine( truth )
                         .combine( allele_freq )
                         .combine( Channel.of([[]]) )
-                        .combine( Channel.of(["chr21"]) )
+                        .combine( Channel.of(["chr22"]) )
 
                 input[0] = list_inputs
-                input[1] = Channel.of([[id:"params"],[],"0 0.01 0.05 0.1 0.2 0.5",[],[]])
-                input[2] = 0.9999
-                input[3] = 8
+                input[1] = Channel.of([[id:"params"], [],"0 0.01 0.05 0.1 0.2 0.5", [], [], [], []])
                 """
             }
         }
@@ -102,78 +60,37 @@ nextflow_process {
 
     }
 
-    test("test_list_region") {
+    test("test list of region and rsquare per site") {
         config "./nextflow.config"
 
         when {
+            params {
+                glimpse2_concordance_args = "--gt-val --af-tag AF --out-r2-per-site"
+            }
             process {
                 """
-                allele_freq = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
+                target = Channel.of([
+                    [id: "input"],
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz.csi",checkIfExists:true)
                 ])
-
                 truth = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/vcf/NA12878_GIAB.chr22.vcf.gz.csi",checkIfExists:true)
                 ])
-                list_inputs = GLIMPSE2_PHASE.output.phased_variants
-                        .join( BCFTOOLS_INDEX.out.csi )
-                        .combine( truth )
-                        .combine( allele_freq )
-                        .combine( Channel.of([[]]) )
-                        .combine( Channel.of(["chr21", "chr21"]) )
-
-                input[0] = list_inputs
-                input[1] = Channel.of([[id:"params"],[],"0 0.01 0.05 0.1 0.2 0.5",[],[]])
-                input[2] = 0.9999
-                input[3] = 8
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(
-                    process.out.errors_cal.collect{ file(it[1]).name },
-                    process.out.errors_grp.collect{ file(it[1]).name },
-                    process.out.errors_spl.collect{ file(it[1]).name },
-                    process.out.rsquare_grp.collect{ file(it[1]).name },
-                    process.out.rsquare_spl.collect{ file(it[1]).name },
-                    process.out.versions
-                ).match()
-                }
-            )
-        }
-
-    }
-
-    test("test_r2_per_site") {
-        config "./nextflow_R2.config"
-
-        when {
-            process {
-                """
                 allele_freq = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz",checkIfExists:true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/1000GP.chr21.noNA12878.s.sites.vcf.gz.csi",checkIfExists:true)
-                ])
-
-                truth = Channel.of([
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf",checkIfExists:true),
-                    file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/glimpse/NA12878.chr21.s.bcf.csi",checkIfExists:true)
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz",checkIfExists:true),
+                    file(params.modules_testdata_base_path + "genomics/homo_sapiens/popgen/1000GP.chr22.sites.vcf.gz.csi",checkIfExists:true)
                 ])
-                list_inputs = GLIMPSE2_PHASE.output.phased_variants
-                        .join( BCFTOOLS_INDEX.out.csi )
+                list_inputs = target
                         .combine( truth )
                         .combine( allele_freq )
                         .combine( Channel.of([[]]) )
-                        .combine( Channel.of(["chr21"]) )
+                        .combine( Channel.of([["chr22", "chr22"]]) )
+                        .view()
+
                 input[0] = list_inputs
-                input[1] = Channel.of([[id:"params"],[],"0 0.01 0.05 0.1 0.2 0.5",[],[]])
-                input[2] = 0.9999
-                input[3] = 8
+                input[1] = Channel.of([[id:"params"], [],"0 0.01 0.05 0.1 0.2 0.5", [], [], [], []])
                 """
             }
         }
@@ -189,11 +106,9 @@ nextflow_process {
                     process.out.rsquare_spl.collect{ file(it[1]).name },
                     process.out.rsquare_per_site.collect{ file(it[1]).name },
                     process.out.versions
-                ).match()
-                }
+                ).match() }
             )
         }
 
     }
-
 }
diff --git a/modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap b/modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap
index 12bded93..5e81d44e 100644
--- a/modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap
+++ b/modules/nf-core/glimpse2/concordance/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "test_r2_per_site": {
+    "test glimpse2 concordance": {
         "content": [
             [
                 "input.error.cal.txt.gz"
@@ -16,20 +16,17 @@
             [
                 "input.rsquare.spl.txt.gz"
             ],
-            [
-                "input_r2_sites.txt.gz"
-            ],
             [
                 "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-22T16:23:00.623182365"
+        "timestamp": "2024-12-03T16:22:35.440086384"
     },
-    "test_glimpse2_concordance": {
+    "test list of region and rsquare per site": {
         "content": [
             [
                 "input.error.cal.txt.gz"
@@ -47,40 +44,16 @@
                 "input.rsquare.spl.txt.gz"
             ],
             [
-                "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
-            ]
-        ],
-        "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
-        },
-        "timestamp": "2024-10-22T16:22:26.823581573"
-    },
-    "test_list_region": {
-        "content": [
-            [
-                "input.error.cal.txt.gz"
-            ],
-            [
-                "input.error.grp.txt.gz"
-            ],
-            [
-                "input.error.spl.txt.gz"
-            ],
-            [
-                "input.rsquare.grp.txt.gz"
-            ],
-            [
-                "input.rsquare.spl.txt.gz"
+                "input_r2_sites.txt.gz"
             ],
             [
                 "versions.yml:md5,ba729289bab6b9fbb8c36a620c86bb82"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-22T16:22:43.352729014"
+        "timestamp": "2024-12-03T16:26:35.009071185"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/concordance/tests/nextflow.config b/modules/nf-core/glimpse2/concordance/tests/nextflow.config
index e5721995..f9242b4b 100644
--- a/modules/nf-core/glimpse2/concordance/tests/nextflow.config
+++ b/modules/nf-core/glimpse2/concordance/tests/nextflow.config
@@ -1,6 +1,6 @@
 process {
-    withName: GLIMPSE2_CHUNK {
+    withName: GLIMPSE2_CONCORDANCE {
+        ext.args   = { params.glimpse2_concordance_args}
         ext.prefix = { "${meta.id}" }
     }
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 }
\ No newline at end of file
diff --git a/modules/nf-core/glimpse2/concordance/tests/nextflow_R2.config b/modules/nf-core/glimpse2/concordance/tests/nextflow_R2.config
deleted file mode 100644
index 0ceee00d..00000000
--- a/modules/nf-core/glimpse2/concordance/tests/nextflow_R2.config
+++ /dev/null
@@ -1,7 +0,0 @@
-process {
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
-    withName:GLIMPSE2_CONCORDANCE {
-        ext.args = "--out-r2-per-site"
-    }
-}

From d1e289c920558450d6b3606b9a518ab2579af2b7 Mon Sep 17 00:00:00 2001
From: LouisLeNezet <louislenezet@gmaio.com>
Date: Wed, 4 Dec 2024 11:41:53 +0100
Subject: [PATCH 16/17] Update java version

---
 .github/workflows/ci.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d93a3b47..16b89e86 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -59,6 +59,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:

From 4c846d0ee7af0f0aea7a572e88e513540dbc439b Mon Sep 17 00:00:00 2001
From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
Date: Wed, 4 Dec 2024 11:52:09 +0100
Subject: [PATCH 17/17] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fb034907..65359551 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -81,8 +81,8 @@ Special thanks to [Matthias Hörtenhuber](https://github.com/mashehu), [Mazzalab
 - [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necessary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
 - [#161](https://github.com/nf-core/phaseimpute/pull/161) - Fix `VCF_SPLIT_BCFTOOLS` when only one sample present by updating `BCFTOOLS_PLUGINSPLIT` and adding `BCFTOOLS_QUERY` to get truth samples names for renaming the resulting files.
 - [#162](https://github.com/nf-core/phaseimpute/pull/162) - Fix `fai` usage when provided by `genomes` parameter.
-- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Fix MULTIQC samples names (add post-processing for clean up `FILTER_CHR_DWN`, `FILTER_CHR_INP`, `GAWK_ERROR_SPL`, `GAWK_RSQUARE_SPL`). Fix output panel `publisDir`.
 - [#164](https://github.com/nf-core/phaseimpute/pull/164) - Improve documentation writing
+- [#163](https://github.com/nf-core/phaseimpute/pull/163) - Fix MULTIQC samples names (add post-processing for clean up `FILTER_CHR_DWN`, `FILTER_CHR_INP`, `GAWK_ERROR_SPL`, `GAWK_RSQUARE_SPL`). Fix output panel `publisDir`. Fix java version to `17` in `ci.yml` due to new nextflow version.
 
 ### `Dependencies`