Update nf-tests and language server fixes

CHANGELOG.md

@@ -64,6 +64,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#148](https://github.com/nf-core/phaseimpute/pull/148) - Fix awsfulltest github action for manual dispatch
 - [#149](https://github.com/nf-core/phaseimpute/pull/149) - Remove the map file from the awsfulltest
 - [#152](https://github.com/nf-core/phaseimpute/pull/152) - Fix URLs in the documentation and remove tools citation in the README, use a white background for all images in the documentation.
+- [#153](https://github.com/nf-core/phaseimpute/pull/153) - Update and simplify subworkflows snapshot and check only for files names (no md5sum for bam and vcf files due to timestamp).
 - [#157](https://github.com/nf-core/phaseimpute/pull/157) - Add `chunk_model` as parameter for better control over `GLIMPSE2_CHUNK` and set window size in `GLIMPSE1_CHUNK` and `GLIMPSE2_chunk` to 4mb to reduce number of chunks (empirical).
 
 ### `Fixed`
@@ -74,6 +75,7 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#75](https://github.com/nf-core/phaseimpute/pull/75) - Set frequency computation with VCFFIXUP process as optional with `--compute_freq`. Use Glimpse_chunk on panel vcf to compute the chunk and not makewindows on fasta.
 - [#117](https://github.com/nf-core/phaseimpute/pull/117) - Fix directories in CSV.
 - [#151](https://github.com/nf-core/phaseimpute/pull/151) - Fix `Type not supported: class org.codehaus.groovy.runtime.GStringImpl` error due to `String` test in `getFileExtension()`.
+- [#153](https://github.com/nf-core/phaseimpute/pull/153) - Fix getFileExtension function. Fix image in `usage.md`. Fix small warnings and errors with updated language server. `def` has been added when necesary, `:` use instead of `,` in assertions, `_` added to variables not used in closures, `for` loop replaced by `.each{}`, remove unused code / input.
 
 ### `Dependencies`
 

main.nf

@@ -126,8 +126,7 @@ workflow {
         params.validate_params,
         params.monochrome_logs,
         args,
-        params.outdir,
-        params.input
+        params.outdir
     )
 
     //

modules/local/add_columns/tests/main.nf.test.snap

@@ -43,7 +43,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b25787d2ba80184a94de82cf5cfe8e7a"
+                    "versions.yml:md5,ab0afe509bddeef28fcf8d00db1cec81"
                 ],
                 "txt": [
                     [
@@ -58,15 +58,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b25787d2ba80184a94de82cf5cfe8e7a"
+                    "versions.yml:md5,ab0afe509bddeef28fcf8d00db1cec81"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-17T14:43:39.390342082"
+        "timestamp": "2024-11-06T13:32:32.608346737"
     },
     "Add columns to txt file with missing fields": {
         "content": [
@@ -81,7 +81,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b25787d2ba80184a94de82cf5cfe8e7a"
+                    "versions.yml:md5,ab0afe509bddeef28fcf8d00db1cec81"
                 ],
                 "txt": [
                     [
@@ -93,14 +93,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b25787d2ba80184a94de82cf5cfe8e7a"
+                    "versions.yml:md5,ab0afe509bddeef28fcf8d00db1cec81"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "24.04.3"
         },
-        "timestamp": "2024-07-17T14:44:39.317216249"
+        "timestamp": "2024-11-06T13:32:39.650698807"
     }
 }

modules/local/bam_chr_extract/main.nf

@@ -35,7 +35,6 @@ process BAM_CHR_EXTRACT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt

modules/local/bam_chr_extract/tests/main.nf.test

@@ -15,15 +15,15 @@ nextflow_process {
                 input[0] =  Channel.fromList([
                     [
                         [ id:'test_single_end_bam' ], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.bam', checkIfExists: true)
                     ],
                     [
                         [id: 'test2_paired_end_sorted_bam'], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true)
                     ],
                     [
                         [id: 'test_paired_end_sorted_cram'], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true)
                     ]
                 ])
                 """

modules/local/list_to_file/tests/main.nf.test.snap

@@ -7,8 +7,8 @@
                         {
                             "id": "all"
                         },
-                        "all_id.txt:md5,6ffc4e703a69bb652dc666a8dcae1863",
-                        "all_noid.txt:md5,045a6e673d95a6e8152a1d06959db93a"
+                        "all.id.txt:md5,6ffc4e703a69bb652dc666a8dcae1863",
+                        "all.noid.txt:md5,045a6e673d95a6e8152a1d06959db93a"
                     ]
                 ],
                 "1": [
@@ -19,8 +19,8 @@
                         {
                             "id": "all"
                         },
-                        "all_id.txt:md5,6ffc4e703a69bb652dc666a8dcae1863",
-                        "all_noid.txt:md5,045a6e673d95a6e8152a1d06959db93a"
+                        "all.id.txt:md5,6ffc4e703a69bb652dc666a8dcae1863",
+                        "all.noid.txt:md5,045a6e673d95a6e8152a1d06959db93a"
                     ]
                 ],
                 "versions": [
@@ -30,9 +30,9 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-10-16T16:15:18.4568228"
+        "timestamp": "2024-11-06T13:55:57.105169612"
     },
     "Content_withid": {
         "content": [

modules/local/vcf_chr_extract/main.nf

@@ -36,7 +36,6 @@ process VCF_CHR_EXTRACT {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt

modules/local/vcf_chr_extract/tests/main.nf.test

@@ -15,15 +15,15 @@ nextflow_process {
                 input[0] = Channel.fromList([
                     [
                         [id:'test_bcf'], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_bcf'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true)
                     ],
                     [
                         [id: 'test2_vcf'], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test2_vcf'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true)
                     ],
                     [
                         [id: 'test2_haplotc_vcf_gz'], // meta map
-                        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true)
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists: true)
                     ]
                 ])
                 """

subworkflows/local/bam_chr_rename_samtools/main.nf

@@ -13,6 +13,7 @@ workflow BAM_CHR_RENAME_SAMTOOLS {
     SAMTOOLS_REHEADER(
         ch_bam.map{
             meta, bam, index, prefix ->
+            def cmd = ""
             if (prefix == "nochr") {
                 cmd = 'sed -E "s/^(@SQ.*\\tSN:)chr/\\1/"'
             } else if (prefix == "chr") {

subworkflows/local/bam_chr_rename_samtools/tests/main.nf.test

@@ -24,14 +24,14 @@ nextflow_workflow {
                 input[0] = Channel.fromList([
                     [
                         [id: "test_paired"],
-                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExist:true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExist:true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExist:true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExist:true),
                         "nochr"
                     ],
                     [
                         [id: "test_MT"],
-                        file(params.test_data['homo_sapiens']['illumina']['test_illumina_mt_bam'], checkIfExist:true),
-                        file(params.test_data['homo_sapiens']['illumina']['test_illumina_mt_bam_bai'], checkIfExist:true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam', checkIfExist:true),
+                        file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai', checkIfExist:true),
                         "nochr"
                     ],
                 ])
@@ -42,11 +42,17 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() },
-                { assert snapshot(workflow.out.bam_renamed.collect{
-                    bam(it[1]).getHeader().findAll { it.startsWith ("@SQ") }
-                    }).match("headernochr")
-                }
+                { assert snapshot(
+                    workflow.out.versions,
+                    workflow.out.bam_renamed.collect{[
+                        it[0],
+                        path(it[1]).getFileName().toString(),
+                        path(it[2]).getFileName().toString()
+                    ] },
+                    workflow.out.bam_renamed.collect{
+                        bam(it[1]).getHeader().findAll { it.startsWith ("@SQ") }
+                    }
+                ).match() }
             )
         }
     }
@@ -60,14 +66,14 @@ nextflow_workflow {
                     input[0] = Channel.fromList([
                         [
                             [id: "test_paired"],
-                            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExist:true),
-                            file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExist:true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExist:true),
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExist:true),
                             "nochr"
                         ],
                         [
                             [id: "test_MT"],
-                            file(params.test_data['homo_sapiens']['illumina']['test_illumina_mt_bam'], checkIfExist:true),
-                            file(params.test_data['homo_sapiens']['illumina']['test_illumina_mt_bam_bai'], checkIfExist:true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam', checkIfExist:true),
+                            file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test_illumina_mt.bam.bai', checkIfExist:true),
                             "nochr"
                         ],
                     ])
@@ -87,11 +93,17 @@ nextflow_workflow {
         then {
             assertAll(
                 { assert workflow.success },
-                { assert snapshot(workflow.out).match() },
-                { assert snapshot(workflow.out.bam_renamed.collect{
-                    bam(it[1]).getHeader().findAll { it.startsWith ("@SQ") }
-                    }).match("headerwithchr")
-                }
+                { assert snapshot(
+                    workflow.out.versions,
+                    workflow.out.bam_renamed.collect{[
+                        it[0],
+                        path(it[1]).getFileName().toString(),
+                        path(it[2]).getFileName().toString()
+                    ] },
+                    workflow.out.bam_renamed.collect{
+                        bam(it[1]).getHeader().findAll { it.startsWith ("@SQ") }
+                    }
+                ).match() }
             )
         }
     }