Updated modules and subworkflows

Plant-Food-Research-Open · Feb 28, 2024 · 39f6854 · 39f6854
1 parent cb325c0
commit 39f6854
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Showing 15 changed files with 414 additions and 158 deletions.
diff --git a/modules.json b/modules.json
@@ -7,17 +7,17 @@
                 "pfr": {
                     "bwa/index": {
                         "branch": "main",
-                        "git_sha": "4b9da80b1e4c16067babd97554bea42d7cd9ca85",
+                        "git_sha": "6410ddc6dfcee5ed480f47199cbd527662cdf5fe",
                         "installed_by": ["fastq_bwa_mem_samblaster"]
                     },
                     "bwa/mem": {
                         "branch": "main",
-                        "git_sha": "835879b8f174bb4d2c5534d0381ffbe62cc1b060",
+                        "git_sha": "6410ddc6dfcee5ed480f47199cbd527662cdf5fe",
                         "installed_by": ["fastq_bwa_mem_samblaster"]
                     },
                     "cat/cat": {
                         "branch": "main",
-                        "git_sha": "4b9da80b1e4c16067babd97554bea42d7cd9ca85",
+                        "git_sha": "6410ddc6dfcee5ed480f47199cbd527662cdf5fe",
                         "installed_by": ["fasta_ltrretriever_lai"]
                     },
                     "custom/checkgff3fastacorrespondence": {
@@ -57,7 +57,7 @@
                     },
                     "ltrharvest": {
                         "branch": "main",
-                        "git_sha": "835879b8f174bb4d2c5534d0381ffbe62cc1b060",
+                        "git_sha": "6410ddc6dfcee5ed480f47199cbd527662cdf5fe",
                         "installed_by": ["fasta_ltrretriever_lai"]
                     },
                     "ltrretriever/lai": {
@@ -72,7 +72,7 @@
                     },
                     "samblaster": {
                         "branch": "main",
-                        "git_sha": "73358a6712178b9a67c39f92e65e8144b5880eae",
+                        "git_sha": "6410ddc6dfcee5ed480f47199cbd527662cdf5fe",
                         "installed_by": ["fastq_bwa_mem_samblaster"]
                     }
                 }
@@ -81,7 +81,7 @@
                 "pfr": {
                     "fasta_ltrretriever_lai": {
                         "branch": "main",
-                        "git_sha": "154661d7c1769532ff7b5f11259644ec200dd47d",
+                        "git_sha": "60ee50c79f8f868fe0b2e48cba543ad1d8fa89b2",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_bwa_mem_samblaster": {

diff --git a/modules/pfr/bwa/index/tests/main.nf.test b/modules/pfr/bwa/index/tests/main.nf.test
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [id: 'test'],
-                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
                 """
             }

diff --git a/modules/pfr/bwa/mem/tests/main.nf.test b/modules/pfr/bwa/mem/tests/main.nf.test
@@ -18,7 +18,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [id: 'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -31,7 +31,7 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = BWA_INDEX.out.index
@@ -58,7 +58,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [id: 'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -71,7 +71,7 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:true ], // meta map
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = BWA_INDEX.out.index
@@ -98,7 +98,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [id: 'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -111,8 +111,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = BWA_INDEX.out.index
@@ -139,7 +139,7 @@ nextflow_process {
                     """
                     input[0] = [
                         [id: 'test'],
-                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                     ]
                     """
                 }
@@ -152,8 +152,8 @@ nextflow_process {
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
                     [
-                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
                     ]
                 ]
                 input[1] = BWA_INDEX.out.index

diff --git a/modules/pfr/cat/cat/tests/main.nf.test b/modules/pfr/cat/cat/tests/main.nf.test
@@ -19,8 +19,8 @@ nextflow_process {
                     [
                         [ id:'genome', single_end:true ],
                         [
-                            file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)
                         ]
                     ]
                 """
@@ -45,8 +45,8 @@ nextflow_process {
                     [
                         [ id:'test', single_end:true ],
                         [
-                            file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)
                         ]
                     ]
                 """
@@ -72,8 +72,8 @@ nextflow_process {
                     [
                         [ id:'test', single_end:true ],
                         [
-                            file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                         ]
                     ]
                 """
@@ -83,7 +83,8 @@ nextflow_process {
             def lines = path(process.out.file_out.get(0).get(1)).linesGzip
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") },
+                { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")}
             )
         }
     }
@@ -101,8 +102,8 @@ nextflow_process {
                     [
                         [ id:'test', single_end:true ],
                         [
-                            file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/last/contigs.genome.maf.gz', checkIfExists: true)
                         ]
                     ]
                 """
@@ -130,8 +131,8 @@ nextflow_process {
                     [
                         [ id:'test', single_end:true ],
                         [
-                            file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
-                            file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true)
                         ]
                     ]
                 """
@@ -141,7 +142,8 @@ nextflow_process {
             def lines = path(process.out.file_out.get(0).get(1)).linesGzip
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") },
+                { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")}
             )
         }
     }
@@ -158,7 +160,7 @@ nextflow_process {
                     [
                         [ id:'test', single_end:true ],
                         [
-                            file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                         ]
                     ]
                 """
@@ -174,4 +176,3 @@ nextflow_process {
         }
     }
 }
-
diff --git a/modules/pfr/cat/cat/tests/main.nf.test.snap b/modules/pfr/cat/cat/tests/main.nf.test.snap
@@ -1,4 +1,10 @@
 {
+    "test_cat_unzipped_zipped_size": {
+        "content": [
+            375
+        ],
+        "timestamp": "2023-10-16T14:33:08.049445686"
+    },
     "test_cat_unzipped_unzipped": {
         "content": [
             {
@@ -61,36 +67,31 @@
         ],
         "timestamp": "2023-10-16T14:32:49.642741302"
     },
-    "test_cat_zipped_zipped": {
+    "test_cat_zipped_zipped_lines": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.gff3.gz:md5,c439d3b60e7bc03e8802a451a0d9a5d9"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894"
-                ],
-                "file_out": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "test.gff3.gz:md5,c439d3b60e7bc03e8802a451a0d9a5d9"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894"
-                ]
-            }
+            [
+                "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab",
+                "MT192765.1\tGenbank\tgene\t259\t21548\t.\t+\t.\tParent=unknown_transcript_1",
+                "MT192765.1\tGenbank\tCDS\t259\t13461\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1",
+                "MT192765.1\tGenbank\tCDS\t13461\t21548\t.\t+\t0\tParent=unknown_transcript_1;exception=\"ribosomal slippage\";gbkey=CDS;gene=orf1ab;note=\"pp1ab;translated=by -1 ribosomal frameshift\";product=\"orf1ab polyprotein\";protein_id=QIK50426.1",
+                "MT192765.1\tGenbank\tCDS\t21556\t25377\t.\t+\t0\tParent=unknown_transcript_1;gbkey=CDS;gene=S;note=\"structural protein\";product=\"surface glycoprotein\";protein_id=QIK50427.1",
+                "MT192765.1\tGenbank\tgene\t21556\t25377\t.\t+\t.\tParent=unknown_transcript_1"
+            ]
+        ],
+        "timestamp": "2023-10-16T14:32:33.629048645"
+    },
+    "test_cat_unzipped_zipped_lines": {
+        "content": [
+            [
+                ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome",
+                "GTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGT",
+                "GTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAG",
+                "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG",
+                "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT",
+                "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG"
+            ]
         ],
-        "timestamp": "2024-01-12T14:02:02.999254641"
+        "timestamp": "2023-10-16T14:33:08.038830506"
     },
     "test_cat_one_file_unzipped_zipped_lines": {
         "content": [
@@ -105,41 +106,16 @@
         ],
         "timestamp": "2023-10-16T14:33:21.39642399"
     },
-    "test_cat_unzipped_zipped": {
+    "test_cat_zipped_zipped_size": {
         "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "cat.txt.gz:md5,f44b33a0e441ad58b2d3700270e2dbe2"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894"
-                ],
-                "file_out": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": true
-                        },
-                        "cat.txt.gz:md5,f44b33a0e441ad58b2d3700270e2dbe2"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894"
-                ]
-            }
+            78
         ],
-        "timestamp": "2024-01-12T14:08:26.948048418"
+        "timestamp": "2023-10-16T14:32:33.641869244"
     },
     "test_cat_one_file_unzipped_zipped_size": {
         "content": [
             374
         ],
-        "timestamp": "2024-01-12T14:10:22.445700266"
+        "timestamp": "2023-10-16T14:33:21.4094373"
     }
-}
+}
diff --git a/modules/pfr/ltrharvest/meta.yml b/modules/pfr/ltrharvest/meta.yml
@@ -12,13 +12,12 @@ keywords:
   - transposons
   - retrotransposons
 tools:
-  - "edta":
-      description: Extensive de-novo TE Annotator (EDTA)
-      homepage: "https://github.com/oushujun/EDTA"
-      documentation: "https://github.com/oushujun/EDTA"
-      tool_dev_url: "https://github.com/oushujun/EDTA"
-      doi: "10.1186/s13059-019-1905-y"
-      licence: ["GPL v3"]
+  - "LTR_HARVEST_parallel":
+      description: A Perl wrapper for LTR_harvest
+      homepage: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel"
+      documentation: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel"
+      tool_dev_url: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel"
+      licence: ["MIT"]
   - "gt":
       description: "The GenomeTools genome analysis system"
       homepage: "https://genometools.org/index.html"

diff --git a/modules/pfr/samblaster/environment.yml b/modules/pfr/samblaster/environment.yml
@@ -1,9 +1,11 @@
 name: samblaster
+
 channels:
   - conda-forge
   - bioconda
   - defaults
+
 dependencies:
+  - bioconda::htslib=1.19.1
   - bioconda::samblaster=0.1.26
   - bioconda::samtools=1.19.2
-  - bioconda::htslib=1.19.1
diff --git a/modules/pfr/samblaster/meta.yml b/modules/pfr/samblaster/meta.yml
@@ -51,3 +51,4 @@ authors:
   - "@lescai"
 maintainers:
   - "@lescai"
+  - "@gallvp"