Updated fasta_ltrretriever_lai

Plant-Food-Research-Open · Jul 23, 2024 · a1bf0e0 · a1bf0e0
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diff --git a/.editorconfig b/.editorconfig
@@ -39,6 +39,20 @@ insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
 
+# These files are edited and tested upstream in gallvp/modules
+[/modules/gallvp/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+[/subworkflows/gallvp/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
 [/assets/email*]
 indent_size = unset
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,11 +11,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 2. Added min. system requirements [#91](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/91)
 3. Updated modules: `UNTAR`, `MERYL_COUNT`, `GUNZIP`, `MINIMAP2_ALIGN`
 4. Added a test to verify the fix for the bug which resulted in a pipeline crash for assemblies without LTRs
-5. Locally patched `FASTA_LTRRETRIEVER_LAI` sub-workflow to emit the `LTRRETRIEVER_LTRRETRIEVER` log as one of the outputs
-6. Locally patched `LTRRETRIEVER_LTRRETRIEVER` module to not fail when `LTR_retriever` exits with an error
-7. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
-8. Updated `SYRI` to 1.7.0 [#104](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/104)
-9. Added a script to automatically check for updates on GitHub/GitLab and post issues
+5. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
+6. Updated `SYRI` to 1.7.0 [#104](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/104)
+7. Added a script to automatically check for updates on GitHub/GitLab and post issues
 
 ### `Fixed`
 

diff --git a/modules.json b/modules.json
@@ -5,12 +5,56 @@
         "https://github.com/GallVp/nxf-components.git": {
             "modules": {
                 "gallvp": {
+                    "cat/cat": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "custom/restoregffids": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "custom/shortenfastaids": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "ltrfinder": {
+                        "branch": "main",
+                        "git_sha": "db7fb043c5557cf06a49a1edbed16e282a7dffb2",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "ltrharvest": {
+                        "branch": "main",
+                        "git_sha": "db7fb043c5557cf06a49a1edbed16e282a7dffb2",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "ltrretriever/lai": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
+                    "ltrretriever/ltrretriever": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["fasta_ltrretriever_lai"]
+                    },
                     "syri": {
                         "branch": "main",
                         "git_sha": "836bb223521eeaa08d65c1b7f4b82be1272a1964",
                         "installed_by": ["modules"]
                     }
                 }
+            },
+            "subworkflows": {
+                "gallvp": {
+                    "fasta_ltrretriever_lai": {
+                        "branch": "main",
+                        "git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
+                        "installed_by": ["subworkflows"]
+                    }
+                }
             }
         },
         "https://github.com/PlantandFoodResearch/nxf-modules.git": {
@@ -36,26 +80,11 @@
                         "git_sha": "d158062346649b5d55bccef77f4bbd0468760aff",
                         "installed_by": ["fastq_bwa_mem_samblaster"]
                     },
-                    "cat/cat": {
-                        "branch": "main",
-                        "git_sha": "10b046eaac396f279c08e7e2bb067482ccd9c74e",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
                     "custom/relabelfasta": {
                         "branch": "main",
                         "git_sha": "0421bdeb1d7a71dce12e0af7dc18aea26e548074",
                         "installed_by": ["modules"]
                     },
-                    "custom/restoregffids": {
-                        "branch": "main",
-                        "git_sha": "da7a50af5eaac9601e23f33e00bf24e61f9c27ab",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "custom/shortenfastaids": {
-                        "branch": "main",
-                        "git_sha": "e9ec2e4c48ead3d760c8e13950c568c19ae86b8b",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
                     "gffread": {
                         "branch": "main",
                         "git_sha": "c3ef9317fe867609f5927588fbf17e3c3ebf389c",
@@ -76,26 +105,6 @@
                         "git_sha": "ffd39a616c84c814fdfb2a865e9fbbb06e5343d9",
                         "installed_by": ["gff3_gt_gff3_gff3validator_stat", "modules"]
                     },
-                    "ltrfinder": {
-                        "branch": "main",
-                        "git_sha": "10b046eaac396f279c08e7e2bb067482ccd9c74e",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "ltrharvest": {
-                        "branch": "main",
-                        "git_sha": "10b046eaac396f279c08e7e2bb067482ccd9c74e",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "ltrretriever/lai": {
-                        "branch": "main",
-                        "git_sha": "10b046eaac396f279c08e7e2bb067482ccd9c74e",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
-                    "ltrretriever/ltrretriever": {
-                        "branch": "main",
-                        "git_sha": "10b046eaac396f279c08e7e2bb067482ccd9c74e",
-                        "installed_by": ["fasta_ltrretriever_lai"]
-                    },
                     "merqury/hapmers": {
                         "branch": "main",
                         "git_sha": "46b70684b6ae0ac60cae154c61796b293707db64",
@@ -125,11 +134,6 @@
                         "git_sha": "0e4afaff4964485d2d93f1115c5254a99765b9c1",
                         "installed_by": ["subworkflows"]
                     },
-                    "fasta_ltrretriever_lai": {
-                        "branch": "main",
-                        "git_sha": "e9ec2e4c48ead3d760c8e13950c568c19ae86b8b",
-                        "installed_by": ["subworkflows"]
-                    },
                     "fastq_bwa_mem_samblaster": {
                         "branch": "main",
                         "git_sha": "d158062346649b5d55bccef77f4bbd0468760aff",

diff --git a/modules/pfr/cat/cat/environment.yml → modules/gallvp/cat/cat/environment.yml b/modules/pfr/cat/cat/environment.yml → modules/gallvp/cat/cat/environment.yml
diff --git a/modules/pfr/cat/cat/main.nf → modules/gallvp/cat/cat/main.nf b/modules/pfr/cat/cat/main.nf → modules/gallvp/cat/cat/main.nf
@@ -76,4 +76,3 @@ def getFileSuffix(filename) {
     def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/
     return match ? match[0][1] : filename.substring(filename.lastIndexOf('.'))
 }
-
diff --git a/modules/pfr/cat/cat/meta.yml → modules/gallvp/cat/cat/meta.yml b/modules/pfr/cat/cat/meta.yml → modules/gallvp/cat/cat/meta.yml
diff --git a/modules/pfr/cat/cat/tests/main.nf.test → modules/gallvp/cat/cat/tests/main.nf.test b/modules/pfr/cat/cat/tests/main.nf.test → modules/gallvp/cat/cat/tests/main.nf.test
@@ -4,7 +4,7 @@ nextflow_process {
     script "../main.nf"
     process "CAT_CAT"
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_gallvp"
     tag "cat"
     tag "cat/cat"
 
@@ -29,7 +29,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert !process.success },
-                { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") }
+                { assert process.stdout.toString().contains("The name of the input file can't be the same as for the output prefix") },
+                { assert snapshot(process.out.versions).match() }
             )
         }
     }
@@ -83,8 +84,12 @@ nextflow_process {
             def lines = path(process.out.file_out.get(0).get(1)).linesGzip
             assertAll(
                 { assert process.success },
-                { assert snapshot(lines[0..5]).match("test_cat_zipped_zipped_lines") },
-                { assert snapshot(lines.size()).match("test_cat_zipped_zipped_size")}
+                { assert snapshot(
+                    lines[0..5],
+                    lines.size(),
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -142,8 +147,12 @@ nextflow_process {
             def lines = path(process.out.file_out.get(0).get(1)).linesGzip
             assertAll(
                 { assert process.success },
-                { assert snapshot(lines[0..5]).match("test_cat_unzipped_zipped_lines") },
-                { assert snapshot(lines.size()).match("test_cat_unzipped_zipped_size")}
+                { assert snapshot(
+                    lines[0..5],
+                    lines.size(),
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
@@ -170,9 +179,13 @@ nextflow_process {
             def lines = path(process.out.file_out.get(0).get(1)).linesGzip
             assertAll(
                 { assert process.success },
-                { assert snapshot(lines[0..5]).match("test_cat_one_file_unzipped_zipped_lines") },
-                { assert snapshot(lines.size()).match("test_cat_one_file_unzipped_zipped_size")}
+                { assert snapshot(
+                    lines[0..5],
+                    lines.size(),
+                    process.out.versions
+                    ).match()
+                }
             )
         }
     }
-}
+}
diff --git a/modules/pfr/cat/cat/tests/main.nf.test.snap → ...es/gallvp/cat/cat/tests/main.nf.test.snap b/modules/pfr/cat/cat/tests/main.nf.test.snap → ...es/gallvp/cat/cat/tests/main.nf.test.snap
@@ -1,10 +1,4 @@
 {
-    "test_cat_unzipped_zipped_size": {
-        "content": [
-            375
-        ],
-        "timestamp": "2023-10-16T14:33:08.049445686"
-    },
     "test_cat_unzipped_unzipped": {
         "content": [
             {
@@ -34,6 +28,10 @@
                 ]
             }
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
         "timestamp": "2023-10-16T14:32:18.500464399"
     },
     "test_cat_zipped_unzipped": {
@@ -65,9 +63,13 @@
                 ]
             }
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
         "timestamp": "2023-10-16T14:32:49.642741302"
     },
-    "test_cat_zipped_zipped_lines": {
+    "test_cat_zipped_zipped": {
         "content": [
             [
                 "MT192765.1\tGenbank\ttranscript\t259\t29667\t.\t+\t.\tID=unknown_transcript_1;geneID=orf1ab;gene_name=orf1ab",
@@ -76,11 +78,31 @@
                 "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"
+            ],
+            78,
+            [
+                "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:51:46.802978"
+    },
+    "test_cat_name_conflict": {
+        "content": [
+            [
+
             ]
         ],
-        "timestamp": "2023-10-16T14:32:33.629048645"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:51:29.45394"
     },
-    "test_cat_unzipped_zipped_lines": {
+    "test_cat_one_file_unzipped_zipped": {
         "content": [
             [
                 ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome",
@@ -89,11 +111,19 @@
                 "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG",
                 "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT",
                 "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG"
+            ],
+            374,
+            [
+                "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894"
             ]
         ],
-        "timestamp": "2023-10-16T14:33:08.038830506"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:52:02.774016"
     },
-    "test_cat_one_file_unzipped_zipped_lines": {
+    "test_cat_unzipped_zipped": {
         "content": [
             [
                 ">MT192765.1 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/PC00101P/2020, complete genome",
@@ -102,20 +132,16 @@
                 "TAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGG",
                 "GTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTT",
                 "ACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAG"
+            ],
+            375,
+            [
+                "versions.yml:md5,115ed6177ebcff24eb99d503fa5ef894"
             ]
         ],
-        "timestamp": "2023-10-16T14:33:21.39642399"
-    },
-    "test_cat_zipped_zipped_size": {
-        "content": [
-            78
-        ],
-        "timestamp": "2023-10-16T14:32:33.641869244"
-    },
-    "test_cat_one_file_unzipped_zipped_size": {
-        "content": [
-            374
-        ],
-        "timestamp": "2023-10-16T14:33:21.4094373"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-22T11:51:57.581523"
     }
 }
diff --git a/...cat/tests/nextflow_unzipped_zipped.config → ...cat/tests/nextflow_unzipped_zipped.config b/...cat/tests/nextflow_unzipped_zipped.config → ...cat/tests/nextflow_unzipped_zipped.config
diff --git a/...cat/tests/nextflow_zipped_unzipped.config → ...cat/tests/nextflow_zipped_unzipped.config b/...cat/tests/nextflow_zipped_unzipped.config → ...cat/tests/nextflow_zipped_unzipped.config
diff --git a/modules/pfr/cat/cat/tests/tags.yml → modules/gallvp/cat/cat/tests/tags.yml b/modules/pfr/cat/cat/tests/tags.yml → modules/gallvp/cat/cat/tests/tags.yml
diff --git a/.../pfr/custom/restoregffids/environment.yml → ...llvp/custom/restoregffids/environment.yml b/.../pfr/custom/restoregffids/environment.yml → ...llvp/custom/restoregffids/environment.yml
diff --git a/modules/pfr/custom/restoregffids/main.nf → modules/gallvp/custom/restoregffids/main.nf b/modules/pfr/custom/restoregffids/main.nf → modules/gallvp/custom/restoregffids/main.nf
diff --git a/modules/pfr/custom/restoregffids/meta.yml → modules/gallvp/custom/restoregffids/meta.yml b/modules/pfr/custom/restoregffids/meta.yml → modules/gallvp/custom/restoregffids/meta.yml
diff --git a/...estoregffids/templates/restore_gff_ids.py → ...estoregffids/templates/restore_gff_ids.py b/...estoregffids/templates/restore_gff_ids.py → ...estoregffids/templates/restore_gff_ids.py
diff --git a/...r/custom/restoregffids/tests/main.nf.test → ...p/custom/restoregffids/tests/main.nf.test b/...r/custom/restoregffids/tests/main.nf.test → ...p/custom/restoregffids/tests/main.nf.test
@@ -5,7 +5,7 @@ nextflow_process {
     process "CUSTOM_RESTOREGFFIDS"
 
     tag "modules"
-    tag "modules_nfcore"
+    tag "modules_gallvp"
     tag "custom"
     tag "custom/restoregffids"
 
@@ -15,7 +15,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
                 ]
                 input[1] = Channel.of('Chr1\tMT192765.1').collectFile(name: 'id_map.tsv', newLine: true)
                 """
@@ -43,7 +43,7 @@ nextflow_process {
                 """
                 input[0] = [
                     [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true)
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true)
                 ]
                 input[1] = Channel.of('Chr1\tMT192765.1').collectFile(name: 'id_map.tsv', newLine: true)
                 """

diff --git a/...tom/restoregffids/tests/main.nf.test.snap → ...tom/restoregffids/tests/main.nf.test.snap b/...tom/restoregffids/tests/main.nf.test.snap → ...tom/restoregffids/tests/main.nf.test.snap
diff --git a/...fr/custom/shortenfastaids/environment.yml → ...vp/custom/shortenfastaids/environment.yml b/...fr/custom/shortenfastaids/environment.yml → ...vp/custom/shortenfastaids/environment.yml
diff --git a/modules/pfr/custom/shortenfastaids/main.nf → ...les/gallvp/custom/shortenfastaids/main.nf b/modules/pfr/custom/shortenfastaids/main.nf → ...les/gallvp/custom/shortenfastaids/main.nf
diff --git a/modules/pfr/custom/shortenfastaids/meta.yml → ...es/gallvp/custom/shortenfastaids/meta.yml b/modules/pfr/custom/shortenfastaids/meta.yml → ...es/gallvp/custom/shortenfastaids/meta.yml
Original file line number	Diff line number	Diff line change
Expand Up		@@ -76,4 +76,3 @@ def getFileSuffix(filename) {
		def match = filename =~ /^.*?((\.\w{1,5})?(\.\w{1,5}\.gz$))/
		return match ? match[0][1] : filename.substring(filename.lastIndexOf('.'))
		}