Merge pull request #474 from nf-core/disable-gunzip-publish

Disable gunzip publish
nf-core · Nov 28, 2024 · c9ba51a · c9ba51a
2 parents d10699e + 79f1a64
commit c9ba51a
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Showing 23 changed files with 101 additions and 143 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 - 🐛 fix fasta gunzip output [#462](https://github.com/nf-core/methylseq/pull/457)
 - 🐛 fix bismark/align not resuming from cache [#461](https://github.com/nf-core/methylseq/pull/457)
+- 🐛 disable gunzip publish by default (https://github.com/nf-core/methylseq/pull/474)
 
 ### Pipeline Updates
 

diff --git a/conf/modules/gunzip.config b/conf/modules/gunzip.config
@@ -0,0 +1,12 @@
+process {
+    withName: GUNZIP {
+        publishDir = [
+            [
+                path: { "${params.outdir}/gunzip/" },
+                mode: params.publish_dir_mode,
+                pattern: "*.{fa,fasta}",
+                enabled: false
+            ]
+        ]
+    }
+}
diff --git a/main.nf b/main.nf
@@ -72,9 +72,11 @@ workflow NFCORE_METHYLSEQ {
         FASTA_INDEX_BISMARK_BWAMETH.out.bismark_index,
         FASTA_INDEX_BISMARK_BWAMETH.out.bwameth_index,
     )
+    ch_versions = ch_versions.mix(METHYLSEQ.out.versions)
+
     emit:
-    multiqc_report = METHYLSEQ.out.multiqc_report // channel: /path/to/multiqc_report.html
-    versions       = ch_versions                  // channel: [version1, version2, ...]
+    multiqc_report = METHYLSEQ.out.multiqc_report // channel: [ path(multiqc_report.html )  ]
+    versions       = ch_versions                  // channel: [ path(versions.yml) ]
 
 }
 /*

diff --git a/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config b/subworkflows/nf-core/fasta_index_bismark_bwameth/nextflow.config
diff --git a/tests/bismark_emseq_clip_r1.nf.test.snap b/tests/bismark_emseq_clip_r1.nf.test.snap
@@ -111,8 +111,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark",
                 "multiqc/bismark/multiqc_data",
@@ -309,7 +307,6 @@
                 "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,f64ef957cbd73eb084e00d72065f4d9e",
                 "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,c9263685b01da6d8ca5df0c0758dc220",
                 "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,747b1dfc8d64866106d9423e6fd34d91",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,670008662fcb3aeb28e1a83d79d30418",
                 "bismark_alignment.txt:md5,9ea891969967030c3089b047f5a898fb",
                 "bismark_deduplication.txt:md5,6be5ee75673e5dcc870d49fe938394c3",
@@ -361,8 +358,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T16:48:43.85530348"
+        "timestamp": "2024-11-28T09:30:17.226120765"
     }
 }
diff --git a/tests/bismark_hisat.nf.test.snap b/tests/bismark_hisat.nf.test.snap
@@ -121,8 +121,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark_hisat",
                 "multiqc/bismark_hisat/multiqc_data",
@@ -319,7 +317,6 @@
                 "SRR389222_sub1_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,30d4e3aec9220b886a6ac17630f48ef3",
                 "SRR389222_sub2_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,8519a3e58f6047f71e8cf09991482332",
                 "SRR389222_sub3_trimmed_bismark_hisat2.deduplicated_splitting_report.txt:md5,e6144ca656936c6ee6e7281a1192fa78",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,233409b9665cb851aca3b6b4511ff757",
                 "bismark_alignment.txt:md5,3acfd1a751bef6696b6fa095d0631bb6",
                 "bismark_deduplication.txt:md5,c025b4368b08f9e623624908632e44a1",
@@ -371,8 +368,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T16:50:33.026655728"
+        "timestamp": "2024-11-28T09:32:04.275412615"
     }
 }
diff --git a/tests/bismark_hisat_rrbs.nf.test.snap b/tests/bismark_hisat_rrbs.nf.test.snap
@@ -110,8 +110,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark_hisat",
                 "multiqc/bismark_hisat/multiqc_data",
@@ -300,7 +298,6 @@
                 "SRR389222_sub1_trimmed_bismark_hisat2_splitting_report.txt:md5,a3ea9994f88802972e25836058ea2b40",
                 "SRR389222_sub2_trimmed_bismark_hisat2_splitting_report.txt:md5,4afad1d4dbe350b2d691561260018247",
                 "SRR389222_sub3_trimmed_bismark_hisat2_splitting_report.txt:md5,bd4b6b3718a4270fc6844862da5c31a7",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,2ed19dff17c089738a62de166f44cf97",
                 "bismark_alignment.txt:md5,0e1ef7bfb853be4fe2471ee1082865c0",
                 "bismark_mbias_CHG_R1.txt:md5,cc89b38a24adcd51363a934964b03892",
@@ -366,8 +363,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T16:54:45.712638793"
+        "timestamp": "2024-11-28T09:35:49.452970243"
     }
 }
diff --git a/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_hisat_save_reference_save_align_intermeds.nf.test.snap
@@ -143,8 +143,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark_hisat",
                 "multiqc/bismark_hisat/multiqc_data",
@@ -360,7 +358,6 @@
                 "BS_GA.8.ht2:md5,33cdeccccebe80329f1fdbee7f5874cb",
                 "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f",
                 "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,233409b9665cb851aca3b6b4511ff757",
                 "bismark_alignment.txt:md5,3acfd1a751bef6696b6fa095d0631bb6",
                 "bismark_deduplication.txt:md5,c025b4368b08f9e623624908632e44a1",
@@ -444,8 +441,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T16:57:16.831873082"
+        "timestamp": "2024-11-28T09:37:31.824088531"
     }
 }
diff --git a/tests/bismark_nomeseq.nf.test.snap b/tests/bismark_nomeseq.nf.test.snap
@@ -135,8 +135,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark",
                 "multiqc/bismark/multiqc_data",
@@ -353,7 +351,6 @@
                 "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,94f18ee855566ef9842b4909e3d3dd88",
                 "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,7c3526e022e97e49677f7428badef420",
                 "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,e8d2bf21731b6ed517c56385061b1dee",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45",
                 "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b",
                 "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76",
@@ -405,8 +402,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T16:59:27.300398291"
+        "timestamp": "2024-11-28T09:39:19.824905083"
     }
 }
diff --git a/tests/bismark_rrbs.nf.test.snap b/tests/bismark_rrbs.nf.test.snap
@@ -110,8 +110,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark",
                 "multiqc/bismark/multiqc_data",
@@ -300,7 +298,6 @@
                 "SRR389222_sub1_trimmed_bismark_bt2_splitting_report.txt:md5,8bf9dc8dd2bb0bc918996edfd02d245e",
                 "SRR389222_sub2_trimmed_bismark_bt2_splitting_report.txt:md5,faeff61aa8cb9d1ba6d67cd4fa7a8587",
                 "SRR389222_sub3_trimmed_bismark_bt2_splitting_report.txt:md5,a5609edd39203f94c5e80dc619b94f68",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,0b7ac7f2e82a9cc4a3362bfcd66a3e26",
                 "bismark_alignment.txt:md5,0a7b6ad94d54f24a91d5126a6acaa9de",
                 "bismark_mbias_CHG_R1.txt:md5,1a54528651513f4bdfa223c22de60c30",
@@ -366,8 +363,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T17:02:08.994971636"
+        "timestamp": "2024-11-28T09:41:20.064526318"
     }
 }
diff --git a/tests/bismark_run_preseq.nf.test.snap b/tests/bismark_run_preseq.nf.test.snap
@@ -111,8 +111,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark",
                 "multiqc/bismark/multiqc_data",
@@ -309,7 +307,6 @@
                 "SRR389222_sub1_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,94f18ee855566ef9842b4909e3d3dd88",
                 "SRR389222_sub2_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,7c3526e022e97e49677f7428badef420",
                 "SRR389222_sub3_trimmed_bismark_bt2.deduplicated_splitting_report.txt:md5,e8d2bf21731b6ed517c56385061b1dee",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45",
                 "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b",
                 "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76",
@@ -361,9 +358,9 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T17:04:32.299955979"
+        "timestamp": "2024-11-28T09:43:14.601958698"
     },
     "Params: bismark | run_preseq with bowtie2-index": {
         "content": [

diff --git a/tests/bismark_run_qualimap.nf.test.snap b/tests/bismark_run_qualimap.nf.test.snap
@@ -307,8 +307,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark",
                 "multiqc/bismark/multiqc_data",
@@ -558,7 +556,7 @@
                 "genome_mapping_quality_histogram.png:md5,74776b1e7e8c8876af1cf89d9dbb5f31",
                 "genome_reads_content_per_read_position.png:md5,c6920dc357411880132c207c7d0aa68d",
                 "genome_uniq_read_starts_histogram.png:md5,8f7549a63eee3d3f022699aaa5bb858d",
-                "qualimapReport.html:md5,2c25df556c43190d52453e76de692a13",
+                "qualimapReport.html:md5,bbc015c0d1f3c41a08c82fb7a6839039",
                 "coverage_across_reference.txt:md5,2bb9eb828acfd71ace8f1e6a2ca124b4",
                 "coverage_histogram.txt:md5,6ee761660a6072e5b6b75b7fe8d2c69e",
                 "duplication_rate_histogram.txt:md5,d5f25ad3572b98880b6904dcf4b3ed25",
@@ -603,7 +601,7 @@
                 "genome_mapping_quality_histogram.png:md5,7ba0db9375d09fd49946b9bca4ba92b4",
                 "genome_reads_content_per_read_position.png:md5,1a6a7717ea948d2518808f72f58ffdef",
                 "genome_uniq_read_starts_histogram.png:md5,395413ab1d0e10af72b116fd8cb12685",
-                "qualimapReport.html:md5,e87a83d69a3d001db49d57a92a7cf25e",
+                "qualimapReport.html:md5,1fe626f663d66a7ce0c6e1e0207d829d",
                 "coverage_across_reference.txt:md5,081ddc3be3349b0c57d9676c03d84803",
                 "coverage_histogram.txt:md5,47b75803a6925e883e254bb91d6220d2",
                 "duplication_rate_histogram.txt:md5,3d06b34e40d1fdeb55c4ad19dc6ddad1",
@@ -645,7 +643,7 @@
                 "genome_mapping_quality_histogram.png:md5,017451f46bc875ac58e7906bf7979956",
                 "genome_reads_content_per_read_position.png:md5,fd94ec5bfe5ca4adfa6ebdeaebe25157",
                 "genome_uniq_read_starts_histogram.png:md5,2f2555ef88c3bda05315469e684f5b19",
-                "qualimapReport.html:md5,91384759d5b7229060c7eea058f74fa1",
+                "qualimapReport.html:md5,af640b29bd28f80bdc0ab6fe7d9c97f4",
                 "coverage_across_reference.txt:md5,a76b3da0ebb2f8bd6c36ec1902cf13f2",
                 "coverage_histogram.txt:md5,ca854c05e9619233b7d95d44051cab80",
                 "duplication_rate_histogram.txt:md5,530bb05c648d610227e121e1e74f41f8",
@@ -687,7 +685,7 @@
                 "genome_mapping_quality_histogram.png:md5,a22ee10fcb9e34a84f607b089855fb92",
                 "genome_reads_content_per_read_position.png:md5,9fa406f353148448f6b9ac11880bc6de",
                 "genome_uniq_read_starts_histogram.png:md5,cf2fe3e30e11e7d6eb2db679cd12dc03",
-                "qualimapReport.html:md5,8753fb47fa86ef92999a0e6ed8b02fd6",
+                "qualimapReport.html:md5,c8114fbb2a63da68111f0d4cbb8a1973",
                 "coverage_across_reference.txt:md5,fb9c989fc6c15d0a8fd0a58b8d3c20ce",
                 "coverage_histogram.txt:md5,8a3f45461442657433914c6a5ecb1301",
                 "duplication_rate_histogram.txt:md5,ec9a705fd3a300b126d556afa14c326b",
@@ -697,7 +695,6 @@
                 "mapping_quality_across_reference.txt:md5,d9bafb5cc106bbd1dc7e31439c618f19",
                 "mapping_quality_histogram.txt:md5,560e85b88f5f90e9ad7ad93ffef42d6f",
                 "versions.yml:md5,bb8bc6f11e6ca441cdb653f077b870c2",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45",
                 "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b",
                 "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76",
@@ -753,18 +750,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T17:08:57.318132441"
-    },
-    "Params: bismark | run_preseq with bowtie2-index": {
-        "content": [
-            36
-        ],
-        "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
-        },
-        "timestamp": "2024-11-27T17:10:56.214178009"
+        "timestamp": "2024-11-28T09:47:26.992492832"
     }
-}
+}
diff --git a/tests/bismark_save_reference_save_align_intermeds.nf.test.snap b/tests/bismark_save_reference_save_align_intermeds.nf.test.snap
@@ -139,8 +139,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark",
                 "multiqc/bismark/multiqc_data",
@@ -352,7 +350,6 @@
                 "BS_GA.rev.2.bt2:md5,fac2f8b39b0e15dec7aa79a0ecf12b49",
                 "genome_mfa.GA_conversion.fa:md5,3dee732bc344fd620c3a7322f52c6a5f",
                 "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,dcbe642c42e31d8e480a2e46b97bbd45",
                 "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b",
                 "bismark_deduplication.txt:md5,db387240d46c09b0b952ed8b54855e76",
@@ -436,8 +433,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T17:13:14.566378345"
+        "timestamp": "2024-11-28T09:49:22.829291635"
     }
 }
diff --git a/tests/bismark_skip_deduplication.nf.test.snap b/tests/bismark_skip_deduplication.nf.test.snap
@@ -110,8 +110,6 @@
                 "fastqc/zips/SRR389222_sub1_fastqc.zip",
                 "fastqc/zips/SRR389222_sub2_fastqc.zip",
                 "fastqc/zips/SRR389222_sub3_fastqc.zip",
-                "gunzip",
-                "gunzip/genome.fa",
                 "multiqc",
                 "multiqc/bismark",
                 "multiqc/bismark/multiqc_data",
@@ -300,7 +298,6 @@
                 "SRR389222_sub1_trimmed_bismark_bt2_splitting_report.txt:md5,15cd690a0366ff38703abf9dd1d5230c",
                 "SRR389222_sub2_trimmed_bismark_bt2_splitting_report.txt:md5,90f7b7a242012045af7fccc5eb94fbf1",
                 "SRR389222_sub3_trimmed_bismark_bt2_splitting_report.txt:md5,beda776b2f0e1faaeafd46f245d273f0",
-                "genome.fa:md5,923a0a268ad29fee3c3437d00f9970de",
                 "bismark-methylation-dp.txt:md5,14edb46f1bc99ddc7f597cb4c6ac9e1c",
                 "bismark_alignment.txt:md5,544a74ea0f32005b0c886af79a6fad5b",
                 "bismark_mbias_CHG_R1.txt:md5,d92f984f52a98ee2943545dd2ae4b860",
@@ -366,8 +363,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-27T17:15:37.365873735"
+        "timestamp": "2024-11-28T09:51:23.826120232"
     }
 }