fix: conda profile by removing md5 check for bam.csi output

Author: imsarath

modules/nf-core/gridss/preprocess/meta.yml

@@ -5,7 +5,6 @@ description: Run the preprocess step of GRIDSS to extract multiple Picard
 keywords:
   - gridss
   - preprocess
-  - picard metrics
   - structural variants
   - bam
 tools:

modules/nf-core/gridss/preprocess/tests/main.nf.test

@@ -50,7 +50,8 @@ nextflow_process {
             def workdir = process.out.preprocess_dir[0][1]
             def prefix  = "test.paired_end.sorted.bam"
             // Picard `# Started on:` and R's PDF `/CreationDate` add per-run timestamps,
-            // and `sv.bam` BGZF blocks are non-reproducible — snapshot only stable parts.
+            // and `sv.bam`/`sv.bam.csi` BGZF blocks differ across conda/docker — snapshot only stable parts.
+            // Presence of `sv.bam` and `sv.bam.csi` is covered by the directory listing snapshot.
             def stripPicardHeaderMd5 = { f -> "${file(f).name}:md5,${listToMD5(path(f).readLines().findAll { !it.startsWith("#") })}" }
 
             assertAll(
@@ -59,7 +60,6 @@ nextflow_process {
                     process.out.preprocess_dir.collect { meta, dir -> [meta, file(dir).list().findAll { it.startsWith(prefix) }.sort()] },
                     path("${workdir}/${prefix}.computesamtags.changes.tsv"),
                     path("${workdir}/${prefix}.coverage.blacklist.bed"),
-                    path("${workdir}/${prefix}.sv.bam.csi"),
                     stripPicardHeaderMd5("${workdir}/${prefix}.cigar_metrics"),
                     stripPicardHeaderMd5("${workdir}/${prefix}.idsv_metrics"),
                     stripPicardHeaderMd5("${workdir}/${prefix}.insert_size_metrics"),

modules/nf-core/gridss/preprocess/tests/main.nf.test.snap

@@ -30,10 +30,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-12T12:49:58.032375609",
+        "timestamp": "2026-06-12T14:30:07.433688807",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.3"
         }
     },
     "human - bam - bwa": {
@@ -59,7 +59,6 @@
             ],
             "test.paired_end.sorted.bam.computesamtags.changes.tsv:md5,ce0a87ccee35f990cd878e12a8a84bae",
             "test.paired_end.sorted.bam.coverage.blacklist.bed:md5,63a1da1606bf23357ad6b1b166c21651",
-            "test.paired_end.sorted.bam.sv.bam.csi:md5,cc1f8720e292f8470b608d7ae9547311",
             "test.paired_end.sorted.bam.cigar_metrics:md5,29b9a700b9da9f2cb23e199e8c15af31",
             "test.paired_end.sorted.bam.idsv_metrics:md5,eeee010100dcea8b9f9eeeac44f8d142",
             "test.paired_end.sorted.bam.insert_size_metrics:md5,4a7d860f1073a82c093373bdbdbd6bf3",
@@ -75,10 +74,10 @@
                 ]
             }
         ],
-        "timestamp": "2026-06-12T12:49:48.647470086",
+        "timestamp": "2026-06-12T14:29:56.150511142",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.4"
+            "nextflow": "26.04.3"
         }
     }
 }