Replace 0.0.2-yy5-c3 with 0.0.3-yy5-c1

sanger-tol · Dec 9, 2024 · 147b88f · 147b88f
1 parent 8805be5
commit 147b88f
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Showing 5 changed files with 98 additions and 26 deletions.
diff --git a/conf/local_testing/test.config b/conf/local_testing/test.config
@@ -0,0 +1,28 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple pipeline test.
+
+    Use as follows:
+        nextflow run sanger-tol/curationpretext -profile test,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'GitHub Test profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+
+    // Limit resources so that this can run on GitHub Actions
+    max_cpus    = 20
+    max_memory  = '30.GB'
+    max_time    = '6.h'
+
+    input       = "/nfs/treeoflife-01/teams/tola/users/dp24/curationpretext/TreeValTinyData/assembly/draft/grTriPseu1.fa"
+    outdir      = "./results"
+    longread    = "/nfs/treeoflife-01/teams/tola/users/dp24/curationpretext/TreeValTinyData/genomic_data/pacbio/"
+    cram        = "/nfs/treeoflife-01/teams/tola/users/dp24/curationpretext/TreeValTinyData/genomic_data/hic-arima/"
+    sample      = "CurationPretextTest"
+    teloseq     = "TTAGGG"
+}
diff --git a/modules.json b/modules.json
@@ -8,117 +8,161 @@
                     "bedtools/bamtobed": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bedtools/genomecov": {
                         "branch": "master",
                         "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bedtools/intersect": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bedtools/makewindows": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bedtools/map": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bedtools/merge": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "gnu/sort": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "minimap2/align": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "minimap2/index": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "pretextmap": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/pretextmap/pretextmap.diff"
                     },
                     "pretextsnapshot": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"],
+                        "installed_by": [
+                            "modules"
+                        ],
                         "patch": "modules/nf-core/pretextsnapshot/pretextsnapshot.diff"
                     },
                     "samtools/faidx": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/merge": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/view": {
                         "branch": "master",
                         "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "seqtk/cutn": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
                         "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "ucsc/bedgraphtobigwig": {
                         "branch": "master",
                         "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "windowmasker/mkcounts": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "windowmasker/ustat": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
diff --git a/modules/local/pretext_graph.nf b/modules/local/pretext_graph.nf
@@ -2,7 +2,7 @@ process PRETEXT_GRAPH {
     tag "$meta.id"
     label 'process_single'
 
-    container "quay.io/sanger-tol/pretext:0.0.2-yy5-c3"
+    container "quay.io/sanger-tol/pretext:0.0.3-yy5-c1"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {

diff --git a/modules/nf-core/pretextmap/main.nf b/modules/nf-core/pretextmap/main.nf
diff --git a/modules/nf-core/pretextmap/pretextmap.diff b/modules/nf-core/pretextmap/pretextmap.diff