Updates to the CICD

sanger-tol · Feb 12, 2025 · c18a84a · c18a84a
1 parent 18f68f9
commit c18a84a
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Showing 8 changed files with 69 additions and 17 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -62,6 +62,12 @@ jobs:
           cp TreeValTinyData/assembly/draft/grTriPseu1.fa TreeValTinyData/assembly/draft/grTriPseu1-hap.fa
           cp TreeValTinyData/assembly/draft/grTriPseu1.fa TreeValTinyData/assembly/draft/grTriPseu1-all_hap.fa
 
+      - name: Download EAR MerquryFK data
+        # Generated .hist and .ktab files (+ hidden files) that is required to test merquryfk
+        run: |
+          curl https://tolit.cog.sanger.ac.uk/test-data/resources/ear/EAR_merquryfk_input.tar.gz | tar xzf -
+          mv EAR_merquryfk_input TreeValTinyData/genomic_data/pacbio/
+
       - name: Install nf-test
         uses: nf-core/setup-nf-test@v1
 

diff --git a/assets/test-local.yaml b/assets/test-local.yaml
@@ -4,12 +4,9 @@ reference_hap1: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/ass
 reference_hap2: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1-hap.fa
 reference_haplotigs: /nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/assembly/draft/grTriPseu1-all_hap.fa
 
-# If a mapped bam already exists use the below + --mapped TRUE on the nextflow command else ignore.
-mapped_bam: []
-
 merquryfk:
-  fastk_hist: "./EMPTY.hist"
-  fastk_ktab: "./EMPTY.ktab"
+  fastk_hist: "/nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/genomic_data/pacbio/kmer.31/gfTriPseu1.50000.k31.hist"
+  fastk_ktab: "/nfs/treeoflife-01/teams/tola/users/dp24/ear/TreeValTinyData/genomic_data/pacbio/kmer.31/"
 
 # Used by both subpipelines
 longread:

diff --git a/assets/test.yaml b/assets/test.yaml
@@ -8,8 +8,8 @@ reference_haplotigs: /home/runner/work/ear/ear/TreeValTinyData/assembly/draft/gr
 mapped_bam: []
 
 merquryfk:
-  fastk_hist: "./EMPTY.hist"
-  fastk_ktab: "./EMPTY.ktab"
+  fastk_hist: "/home/runner/work/ear/ear/TreeValTinyData/genomic_data/pacbio/EAR_merquryfk_input/gfTriPseu1.50000.k31.hist"
+  fastk_ktab: "/home/runner/work/ear/ear/TreeValTinyData/genomic_data/pacbio/EAR_merquryfk_input/"
 
 # Used by both subpipelines
 longread:

diff --git a/conf/test.config b/conf/test.config
@@ -27,5 +27,5 @@ params {
     // Input data for full size test
     // Limit resources so that this can run on GitHub Actions
     input       = "${baseDir}/assets/test.yaml"
-    steps       = "btk,cpretext,merquryfk"
+    steps       = "btk,cpretext"
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -16,4 +16,5 @@ params {
 
     input       = "${projectDir}/assets/test-local.yaml"
     outdir      = "results"
+    steps       = "btk,cpretext"
 }
diff --git a/nf-test.config b/nf-test.config
@@ -11,6 +11,6 @@ config {
         load "[email protected]"
     }
 
-    configFile "conf/test.config"
+    configFile "conf/test_full.config"
     profile "test"
 }
diff --git a/tests/main.nf.test b/tests/main.nf.test
@@ -20,7 +20,7 @@ nextflow_pipeline {
 
             def gfastats = getAllFilesFromDir(params.outdir, include: ['gfastats/*_summary'])
 
-            //def merquryfk = getAllFilesFromDir(params.outdir, include: ['merquryfk/*'])
+            def merquryfk = getAllFilesFromDir(params.outdir, include: ['merquryfk/*'])
 
             assertAll (
                 {assert workflow.success},
@@ -38,9 +38,13 @@ nextflow_pipeline {
                     gfastats,
 
                     // MERQURY_FK is running statistics on the input files
-                    // input files are also split between the two main input haps
-                    // need to actually test merqury first
-                    //merquryfk,
+                    merquryfk.size(),
+                    merquryfk,
+                    merquryfk.any{it.toString().contains("combined_haplos".toString())},
+                    merquryfk.any{it.toString().contains("spectra".toString())},
+                    merquryfk.any{it.toString().contains(".qv".toString())},
+                    merquryfk.any{it.toString().contains(".bed".toString())},
+                    merquryfk.any{it.toString().contains(".stats".toString())}
 
                 ).match()},
             )

diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
@@ -1,33 +1,77 @@
 {
     "Minimal run | No SANGER-TOL-* nested pipelines": {
         "content": [
-            2,
+            3,
             {
                 "CAT_CAT": {
                     "pigz": "2.3.4"
                 },
                 "GFASTATS": {
                     "gfastats": "1.3.6"
                 },
+                "MERQURYFK_MERQURYFK": {
+                    "fastk": "f18a4e6d2207539f7b84461daebc54530a9559b0",
+                    "merquryfk": "8ae344092df5dcaf83cfb7f90f662597a9b1fc61",
+                    "r": "4.2.0"
+                },
                 "Workflow": {
-                    "sanger-tol/ear": "v0.6.2"
+                    "sanger-tol/ear": "v0.7.0"
                 }
             },
             [
                 "gfastats",
                 "gfastats/grTriPseu1.assembly_summary",
+                "merquryfk",
+                "merquryfk/grTriPseu1.combined_haplos.qv",
+                "merquryfk/grTriPseu1.combined_haplos.spectra-cn.fl.png",
+                "merquryfk/grTriPseu1.combined_haplos.spectra-cn.ln.png",
+                "merquryfk/grTriPseu1.combined_haplos.spectra-cn.st.png",
+                "merquryfk/grTriPseu1.combined_haplos_only.bed",
+                "merquryfk/grTriPseu1.completeness.stats",
+                "merquryfk/grTriPseu1.grTriPseu1.qv",
+                "merquryfk/grTriPseu1.grTriPseu1.spectra-cn.fl.png",
+                "merquryfk/grTriPseu1.grTriPseu1.spectra-cn.ln.png",
+                "merquryfk/grTriPseu1.grTriPseu1.spectra-cn.st.png",
+                "merquryfk/grTriPseu1.grTriPseu1_only.bed",
+                "merquryfk/grTriPseu1.qv",
+                "merquryfk/grTriPseu1.spectra-asm.fl.png",
+                "merquryfk/grTriPseu1.spectra-asm.ln.png",
+                "merquryfk/grTriPseu1.spectra-asm.st.png",
                 "pipeline_info",
                 "pipeline_info/ear_software_mqc_versions.yml"
             ],
             1,
             [
                 "grTriPseu1.assembly_summary:md5,49d6ad52839bf6597b0ff6fb9ff01151"
-            ]
+            ],
+            15,
+            [
+                "grTriPseu1.combined_haplos.qv:md5,ee9ad1aea0ad003e5ac866df174902f1",
+                "grTriPseu1.combined_haplos.spectra-cn.fl.png:md5,50bad6b85b8f80b8411b50e4119bc959",
+                "grTriPseu1.combined_haplos.spectra-cn.ln.png:md5,50bad6b85b8f80b8411b50e4119bc959",
+                "grTriPseu1.combined_haplos.spectra-cn.st.png:md5,50bad6b85b8f80b8411b50e4119bc959",
+                "grTriPseu1.combined_haplos_only.bed:md5,04220c269d33e2bbc1122595828d8275",
+                "grTriPseu1.completeness.stats:md5,a3d2d772cc118547335dde59161b9217",
+                "grTriPseu1.grTriPseu1.qv:md5,953ba4f3322475292919671a2393b52d",
+                "grTriPseu1.grTriPseu1.spectra-cn.fl.png:md5,4b0c20fb8c99b0e725d569fc7252078f",
+                "grTriPseu1.grTriPseu1.spectra-cn.ln.png:md5,7f07db43d617056109c2ebab5b47b7cc",
+                "grTriPseu1.grTriPseu1.spectra-cn.st.png:md5,9717069c33da319c45f0d976b3697b66",
+                "grTriPseu1.grTriPseu1_only.bed:md5,9af876714b7666bb628a21dd275d0691",
+                "grTriPseu1.qv:md5,0d51bda46c4cafbeb3c082768beefd6b",
+                "grTriPseu1.spectra-asm.fl.png:md5,50bad6b85b8f80b8411b50e4119bc959",
+                "grTriPseu1.spectra-asm.ln.png:md5,50bad6b85b8f80b8411b50e4119bc959",
+                "grTriPseu1.spectra-asm.st.png:md5,50bad6b85b8f80b8411b50e4119bc959"
+            ],
+            true,
+            true,
+            true,
+            true,
+            true
         ],
         "meta": {
             "nf-test": "0.9.2",
             "nextflow": "24.04.4"
         },
-        "timestamp": "2025-02-07T16:10:18.940156"
+        "timestamp": "2025-02-12T14:49:22.178822"
     }
 }