Add sample name to TRGT output (genomic-medicine-sweden#333)

fellen31 · Sep 11, 2024 · f266b6c · f266b6c
1 parent 56a0efc
commit f266b6c
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Showing 5 changed files with 21 additions and 23 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v0.3.0 - [2024-08-28]
+## v0.3.0 - [2024-08-29]
 
 ### `Added`
 
@@ -68,6 +68,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#323](https://github.com/genomic-medicine-sweden/nallo/pull/323) - Changed `parallel_alignment` to `parallel_alignments` in CI tests as well
 - [#330](https://github.com/genomic-medicine-sweden/nallo/pull/330) - Updated README and version bump
 - [#332](https://github.com/genomic-medicine-sweden/nallo/pull/332) - Changed the PED file input to genmod to include inferred sex from somalier
+- [#333](https://github.com/genomic-medicine-sweden/nallo/pull/333) - Updated TRGT to 0.7.0 and added `meta.id` as output sample name
 
 ### `Removed`
 
@@ -117,6 +118,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | tabix                       | 1.19.1      | 1.20        |
 | echtvar                     | 0.1.7       | 0.2.0       |
 | somalier                    | 0.2.15      | 0.2.18      |
+| TRGT                        | 0.4.0       | 0.7.0       |
 | cadd                        |             | 1.6.post1   |
 | gawk                        |             | 5.3.0       |
 | add_most_severe_consequence |             | v1.0        |

diff --git a/conf/modules/call_repeat_expansions.config b/conf/modules/call_repeat_expansions.config
@@ -24,10 +24,12 @@ process {
         ]
     }
 
-    withName: '.*:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT_TRGT' {
+    withName: '.*:CALL_REPEAT_EXPANSIONS:TRGT' {
+        ext.args = { "--sample-name ${meta.id}" }
+    }
 
+    withName: '.*:CALL_REPEAT_EXPANSIONS:SAMTOOLS_SORT_TRGT' {
         ext.prefix = { "${meta.id}_spanning_sorted" }
-
         publishDir = [
             path: { "${params.outdir}/repeat_calling/trgt/single_sample/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -36,7 +38,6 @@ process {
     }
 
     withName: '.*:CALL_REPEAT_EXPANSIONS:SAMTOOLS_INDEX_TRGT' {
-
         publishDir = [
             path: { "${params.outdir}/repeat_calling/trgt/single_sample/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -45,13 +46,11 @@ process {
     }
 
     withName: '.*:CALL_REPEAT_EXPANSIONS:BCFTOOLS_SORT_TRGT' {
-
         ext.prefix = { "${meta.id}_sorted" }
         ext.args = [
             '--output-type z',
             '--write-index=tbi'
         ].join(' ')
-
         publishDir = [
             path: { "${params.outdir}/repeat_calling/trgt/single_sample/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -60,13 +59,11 @@ process {
     }
 
     withName: '.*:CALL_REPEAT_EXPANSIONS:BCFTOOLS_MERGE' {
-
         ext.args = [
             '--output-type z',
             '--write-index=tbi',
             '--force-single'
         ].join(' ')
-
         publishDir = [
             path: { "${params.outdir}/repeat_calling/trgt/multi_sample/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -75,9 +72,7 @@ process {
     }
 
     withName: '.*:CALL_REPEAT_EXPANSIONS:BCFTOOLS_INDEX_MERGE' {
-
         ext.args = '--tbi'
-
         publishDir = [
             path: { "${params.outdir}/repeat_calling/trgt/multi_sample/${meta.id}" },
             mode: params.publish_dir_mode,

diff --git a/modules/local/trgt/main.nf b/modules/local/trgt/main.nf
@@ -3,11 +3,12 @@ process TRGT {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "pacbio/trgt:0.4.0"
+    container "biocontainers/trgt:0.7.0--hdfd78af_0"
 
     input:
     tuple val(meta), path(bam), path(bai), val(sex)
     tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
     path(repeats)
 
     output:

diff --git a/subworkflows/local/call_repeat_expansions/main.nf b/subworkflows/local/call_repeat_expansions/main.nf
@@ -22,7 +22,7 @@ workflow CALL_REPEAT_EXPANSIONS {
         .set { ch_trgt_input }
 
     // Run TGRT
-    TRGT ( ch_trgt_input, ch_fasta, ch_trgt_bed.map { it[1] } )
+    TRGT ( ch_trgt_input, ch_fasta, ch_fai, ch_trgt_bed.map { it[1] } )
 
     // Sort and index bam
     SAMTOOLS_SORT_TRGT ( TRGT.out.bam, [[],[]] )

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
@@ -40,9 +40,9 @@
             "HG002_Revio.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
             "HG002_Revio.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab",
             "HG002_PacBio_Revio.fastq.gz.tsv.zst:md5,4b073293b3e771d19b4cfdb07909571b",
-            "HG002_Revio_sorted.vcf.gz:md5,bc06de08b8e36b3b48e0d7b9e21df389",
-            "HG002_Revio_sorted.vcf.gz.tbi:md5,08a5c82838264c558eb30726906f47e0",
-            "110181f29066158df34abbad9e3becc8",
+            "HG002_Revio_sorted.vcf.gz:md5,fbb5699b8f74fc105fb154e8fac7bfea",
+            "HG002_Revio_sorted.vcf.gz.tbi:md5,0466518ee265ba63160ed27cee0dec88",
+            "65999ab8f2bc7841de8172468bf23ab6",
             [
                 "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
                 "# The command line was:\tbcftools stats  HG002_Revio.vcf.gz",
@@ -53,7 +53,7 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-08-12T09:45:54.652442138"
+        "timestamp": "2024-08-29T10:42:09.011660883"
     },
     "test profile - multisample": {
         "content": [
@@ -92,9 +92,9 @@
             "HG002_Revio_A.regions.bed.gz:md5,e051f64c7a780d67ea6727a327dd4281",
             "HG002_Revio_A.regions.bed.gz.csi:md5,026eef1c69fb4aa3a1687463fe2088ab",
             "HG002_PacBio_Revio.bam_other.fastq.gz.tsv.zst:md5,4b073293b3e771d19b4cfdb07909571b",
-            "HG002_Revio_A_sorted.vcf.gz:md5,b95e709a27fe1df9ee1487b99f396bf4",
-            "HG002_Revio_A_sorted.vcf.gz.tbi:md5,b1eb1f21f36782089b8e0bb0a54105ed",
-            "110181f29066158df34abbad9e3becc8",
+            "HG002_Revio_A_sorted.vcf.gz:md5,680938d6ebeafe73d8df0b21c0310276",
+            "HG002_Revio_A_sorted.vcf.gz.tbi:md5,a6554ab817e7c232a1554ea85fa00151",
+            "65999ab8f2bc7841de8172468bf23ab6",
             [
                 "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
                 "# The command line was:\tbcftools stats  HG002_Revio_A.vcf.gz",
@@ -132,9 +132,9 @@
             "HG002_Revio_B.regions.bed.gz:md5,deaca22783bd058cdc8756efa25b5f53",
             "HG002_Revio_B.regions.bed.gz.csi:md5,dd9a0d36d71da0d274d1c9ca6f8571ae",
             "HG002_Revio_B.merged.fastq.gz.tsv.zst:md5,0641e175a07429b61710329a2eeef450",
-            "HG002_Revio_B_sorted.vcf.gz:md5,05ae66b46d2f87a2133fcdf93d30f38c",
-            "HG002_Revio_B_sorted.vcf.gz.tbi:md5,244a3f966e3434220cd69fcb04b08d01",
-            "18e3bd1fe43fc17ace2f57db5861498c",
+            "HG002_Revio_B_sorted.vcf.gz:md5,ce617741468f4bc7f504f8f488332098",
+            "HG002_Revio_B_sorted.vcf.gz.tbi:md5,e255a5ea92885967f0c126bddc8ea3b2",
+            "6b0cf3f492ce898398835d1102afd369",
             [
                 "# This file was produced by bcftools stats (1.20+htslib-1.20) and can be plotted using plot-vcfstats.",
                 "# The command line was:\tbcftools stats  HG002_Revio_B.vcf.gz",
@@ -145,6 +145,6 @@
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-08-28T13:37:54.494547598"
+        "timestamp": "2024-08-29T10:45:44.41793623"
     }
 }