Updated snapshots to account for 4 CPUs

Plant-Food-Research-Open · Oct 10, 2024 · beb0c7b · beb0c7b
1 parent b193a4c
commit beb0c7b
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Showing 10 changed files with 152 additions and 144 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -73,6 +73,10 @@ jobs:
         with:
           version: 0.9.0
 
+      - name: Disk space cleanup
+        if: matrix.nf_test_files == 'tests/stub/main.nf.test'
+        uses: jlumbroso/[email protected]
+
       - name: Run nf-test
         run: |
           nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}"

diff --git a/conf/modules.config b/conf/modules.config
@@ -292,23 +292,23 @@ process {
         ]
     }
 
-    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
+    withName: '.*:FQ2HIC:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_RAW' {
         publishDir = [
             path: { "${params.outdir}/hic/fastqc_raw" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
         ]
     }
 
-    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
+    withName: '.*:FQ2HIC:FASTQ_FASTQC_UMITOOLS_FASTP:FASTQC_TRIM' {
         publishDir = [
             path: { "${params.outdir}/hic/fastqc_trim" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals("versions.yml") ? null : filename }
         ]
     }
 
-    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
+    withName: '.*:FQ2HIC:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
         ext.args = params.hic_fastp_ext_args
         publishDir = [
             path: { "${params.outdir}/hic/fastp" },
@@ -321,12 +321,12 @@ process {
         ext.args = '--ignore-case --natural-order'
     }
 
-    withName: '.*:FASTQ_BWA_MEM_SAMBLASTER:BWA_MEM' {
+    withName: '.*:FQ2HIC:FASTQ_BWA_MEM_SAMBLASTER:BWA_MEM' {
         ext.prefix = { "${meta.id}.on.${meta.ref_id}.bwa.mem" }
         ext.args = '-5SP'
     }
 
-    withName: '.*:FASTQ_BWA_MEM_SAMBLASTER:SAMBLASTER' {
+    withName: '.*:FQ2HIC:FASTQ_BWA_MEM_SAMBLASTER:SAMBLASTER' {
         ext.prefix = { "${meta.id}.on.${meta.ref_id}.samblaster" }
         ext.args3 = '-h -F 2316'
     }

diff --git a/modules/gallvp/bwa/mem/tests/main.nf.test.snap b/modules/gallvp/bwa/mem/tests/main.nf.test.snap
@@ -13,14 +13,14 @@
             [
                 "versions.yml:md5,478b816fbd37871f5e8c617833d51d80"
             ],
-            "b6d9cb250261a4c125413c5d867d87a7",
+            "895cf107b1c13b0f0cabc1421a4f5db9",
             "798439cbd7fd81cbcc5078022dc5479d"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-02T12:22:28.051598"
+        "timestamp": "2024-10-10T20:57:38.428887"
     },
     "Single-End Sort": {
         "content": [
@@ -36,14 +36,14 @@
             [
                 "versions.yml:md5,478b816fbd37871f5e8c617833d51d80"
             ],
-            "848434ae4b79cfdcb2281c60b33663ce",
+            "98350949b5a0931930c69cff0e380274",
             "94fcf617f5b994584c4e8d4044e16b4f"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-02T12:22:39.671154"
+        "timestamp": "2024-10-10T20:57:52.438702"
     },
     "Paired-End": {
         "content": [
@@ -59,14 +59,14 @@
             [
                 "versions.yml:md5,478b816fbd37871f5e8c617833d51d80"
             ],
-            "5b34d31be84478761f789e3e2e805e31",
+            "a42d8e219e0df24f3d72a646b7c26dbb",
             "57aeef88ed701a8ebc8e2f0a381b2a6"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-02T12:22:51.919479"
+        "timestamp": "2024-10-10T20:58:05.532827"
     },
     "Paired-End Sort": {
         "content": [
@@ -82,14 +82,14 @@
             [
                 "versions.yml:md5,478b816fbd37871f5e8c617833d51d80"
             ],
-            "69003376d9a8952622d8587b39c3eaae",
+            "ee5c324f68d45c4d01c937b4abbc5de",
             "af8628d9df18b2d3d4f6fd47ef2bb872"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-02T12:23:00.833562"
+        "timestamp": "2024-10-10T20:58:20.859431"
     },
     "Single-end - stub": {
         "content": [
@@ -182,14 +182,14 @@
             [
                 "versions.yml:md5,478b816fbd37871f5e8c617833d51d80"
             ],
-            "5b34d31be84478761f789e3e2e805e31",
+            "a42d8e219e0df24f3d72a646b7c26dbb",
             "57aeef88ed701a8ebc8e2f0a381b2a6"
         ],
         "meta": {
             "nf-test": "0.9.0",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2024-08-02T12:23:09.942545"
+        "timestamp": "2024-10-10T20:58:35.460705"
     },
     "Paired-end - stub": {
         "content": [

diff --git a/modules/gallvp/minimap2/align/tests/main.nf.test.snap b/modules/gallvp/minimap2/align/tests/main.nf.test.snap
@@ -4,8 +4,8 @@
             [
                 "@HD\tVN:1.6\tSO:coordinate",
                 "@SQ\tSN:MT192765.1\tLN:29829",
-                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a genome.fasta -",
-                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam##idx##test.bam.bai --write-index"
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 4 -a genome.fasta -",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 3 -o test.bam##idx##test.bam.bai --write-index"
             ],
             "5d426b9a5f5b2c54f1d7f1e4c238ae94",
             "test.bam.bai",
@@ -14,10 +14,10 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T09:03:00.827260362"
+        "timestamp": "2024-10-10T20:47:38.40726"
     },
     "sarscov2 - bam, fasta, true, 'bai', false, false - stub": {
         "content": [
@@ -236,46 +236,46 @@
             [
                 "@HD\tVN:1.6\tSO:coordinate",
                 "@SQ\tSN:MT192765.1\tLN:29829",
-                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz test_2.fastq.gz",
-                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam"
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 4 -a genome.fasta test_1.fastq.gz test_2.fastq.gz",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 3 -o test.bam"
             ],
             "1bc392244f228bf52cf0b5a8f6a654c9",
             [
                 "versions.yml:md5,3548eeba9066efbf8d78ea99f8d813fd"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-23T11:18:18.964586894"
+        "timestamp": "2024-10-10T20:47:04.155509"
     },
     "sarscov2 - fastq, fasta, true, [], false, false": {
         "content": [
             [
                 "@HD\tVN:1.6\tSO:coordinate",
                 "@SQ\tSN:MT192765.1\tLN:29829",
-                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz",
-                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam"
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 4 -a genome.fasta test_1.fastq.gz",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 3 -o test.bam"
             ],
             "f194745c0ccfcb2a9c0aee094a08750",
             [
                 "versions.yml:md5,3548eeba9066efbf8d78ea99f8d813fd"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-23T11:17:48.667488325"
+        "timestamp": "2024-10-10T20:46:42.073683"
     },
     "sarscov2 - fastq, fasta, true, 'bai', false, false": {
         "content": [
             [
                 "@HD\tVN:1.6\tSO:coordinate",
                 "@SQ\tSN:MT192765.1\tLN:29829",
-                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a genome.fasta test_1.fastq.gz",
-                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam##idx##test.bam.bai --write-index"
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 4 -a genome.fasta test_1.fastq.gz",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 3 -o test.bam##idx##test.bam.bai --write-index"
             ],
             "f194745c0ccfcb2a9c0aee094a08750",
             "test.bam.bai",
@@ -284,29 +284,29 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-23T11:18:02.517416733"
+        "timestamp": "2024-10-10T20:46:53.814566"
     },
     "sarscov2 - bam, fasta, true, [], false, false": {
         "content": [
             [
                 "@HD\tVN:1.6\tSO:coordinate",
                 "@SQ\tSN:MT192765.1\tLN:29829",
-                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a genome.fasta -",
-                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam"
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 4 -a genome.fasta -",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 3 -o test.bam"
             ],
             "5d426b9a5f5b2c54f1d7f1e4c238ae94",
             [
                 "versions.yml:md5,3548eeba9066efbf8d78ea99f8d813fd"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-25T09:02:49.64829488"
+        "timestamp": "2024-10-10T20:47:26.993111"
     },
     "sarscov2 - bam, fasta, true, [], false, false - stub": {
         "content": [
@@ -459,18 +459,18 @@
                 "@SQ\tSN:ERR5069949.3258358\tLN:151",
                 "@SQ\tSN:ERR5069949.1476386\tLN:151",
                 "@SQ\tSN:ERR5069949.2415814\tLN:150",
-                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 2 -a test_1.fastq.gz test_1.fastq.gz",
-                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 1 -o test.bam"
+                "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -t 4 -a test_1.fastq.gz test_1.fastq.gz",
+                "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.20\tCL:samtools sort -@ 3 -o test.bam"
             ],
             "16c1c651f8ec67383bcdee3c55aed94f",
             [
                 "versions.yml:md5,3548eeba9066efbf8d78ea99f8d813fd"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-07-23T11:18:34.246998277"
+        "timestamp": "2024-10-10T20:47:14.585958"
     }
 }