Strict syntax (#123)

* Template update for nf-core/tools version 2.6

* Template update for nf-core/tools version 2.7.2

* update pipeline name

* update pipeline name

* Template update for nf-core/tools version 3.5.1

* fix merge issues

* pre-commit

* ignore the test_data param

* remove stdout from tests and update snapshots

* Channel -> channel

* remove old gridss and annotsv code

* remove old gridss and annotsv code

* fix first syntax problems

* latest syntax fixes

* fix default snap

* fix the last language server issues

Author: nvnieuwk

main.nf

@@ -29,8 +29,6 @@ params.fai                      = getGenomeAttribute('fai')
 params.dict                     = getGenomeAttribute('dict')
 params.gtf                      = getGenomeAttribute('gtf')
 params.vep_cache                = getGenomeAttribute('vep_cache')
-// params.bwa                      = getGenomeAttribute('bwa')
-// params.annotsv_annotations      = getGenomeAttribute('annotsv_annotations')
 params.expansionhunter_catalog  = getGenomeAttribute('expansionhunter_catalog')
 params.qdnaseq_male             = getGenomeAttribute("qdnaseq_male_${params.qdnaseq_bin_size.toInteger() / 1000}kbp".toString())
 params.qdnaseq_female           = getGenomeAttribute("qdnaseq_female_${params.qdnaseq_bin_size.toInteger() / 1000}kbp".toString())
@@ -67,9 +65,9 @@ workflow {
         params.show_hidden
     )
 
-    def ch_multiqc_config          = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
-    def ch_multiqc_custom_config   = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty()
-    def ch_multiqc_logo            = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty()
+    def ch_multiqc_config          = channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+    def ch_multiqc_custom_config   = params.multiqc_config ? channel.fromPath( params.multiqc_config, checkIfExists: true ) : channel.empty()
+    def ch_multiqc_logo            = params.multiqc_logo   ? channel.fromPath( params.multiqc_logo, checkIfExists: true ) : channel.empty()
     def ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
 
     //
@@ -93,9 +91,6 @@ workflow {
         params.qdnaseq_male,
         params.wisecondorx_reference,
         params.vep_cache,
-        // params.annotsv_annotations,
-        // params.annotsv_candidate_genes,
-        // params.annotsv_gene_transcripts,
         params.vcfanno_lua,
         params.vcfanno_resources,
         params.vcfanno_toml,

modules.json

@@ -5,16 +5,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "annotsv/annotsv": {
-                        "branch": "master",
-                        "git_sha": "296d216c3f6384936a6526b6fbed7e6412259fb4",
-                        "installed_by": ["modules"]
-                    },
-                    "annotsv/installannotations": {
-                        "branch": "master",
-                        "git_sha": "296d216c3f6384936a6526b6fbed7e6412259fb4",
-                        "installed_by": ["modules"]
-                    },
                     "bcftools/annotate": {
                         "branch": "master",
                         "git_sha": "2ad29c2aed06d815d9f68ad7ba20b3b1c574ce9c",
@@ -82,25 +72,19 @@
                         "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
                         "installed_by": ["modules"]
                     },
-                    "gridss/gridss": {
-                        "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/gridss/gridss/gridss-gridss.diff"
-                    },
                     "jasminesv": {
                         "branch": "master",
-                        "git_sha": "a33c6de0a147226454c4a52db710826f2d9fafbe",
+                        "git_sha": "671cad06f043fdf5c5aae7c49890ad8ccdacbb04",
                         "installed_by": ["modules"]
                     },
                     "manta/convertinversion": {
                         "branch": "master",
-                        "git_sha": "92bf2a8afa318a64f9d333cf87b510c662fd4274",
+                        "git_sha": "3485512d3930df1fcb66b5f92af639179bdfe4be",
                         "installed_by": ["modules"]
                     },
                     "manta/germline": {
                         "branch": "master",
-                        "git_sha": "ebc1733b77c702f19fe42076a5edfcbaa0d84f66",
+                        "git_sha": "3485512d3930df1fcb66b5f92af639179bdfe4be",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -203,7 +187,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
+                        "git_sha": "ff506dcada6fc826ed0c641dc2ed1e98f7345fbe",
                         "installed_by": ["subworkflows"]
                     }
                 }