Exchange local filtlong module to nf-core/filtlong

conf/modules.config

@@ -178,13 +178,19 @@ process {
     }
 
     withName: FILTLONG {
+        ext.args = [
+            "--min_length ${params.longreads_min_length}",
+            "--keep_percent ${params.longreads_keep_percent}",
+            "--trim",
+            "--length_weight ${params.longreads_length_weight}"
+        ].join(' ').trim()
         publishDir = [
                 path: { "${params.outdir}/QC_longreads/Filtlong" },
                 mode: params.publish_dir_mode,
                 pattern: "*_lr_filtlong.fastq.gz",
                 enabled: params.save_filtlong_reads
             ]
-        ext.prefix = { "${meta.id}_run${meta.run}_lengthfiltered" }
+        ext.prefix = { "${meta.id}_run${meta.run}_lr_filtlong" }
     }
 
     withName: NANOLYSE {

modules.json

@@ -112,6 +112,11 @@
                         "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
                         "installed_by": ["modules"]
                     },
+                    "filtlong": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "freebayes": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",

subworkflows/local/lr_preprocessing.nf

@@ -6,8 +6,7 @@ include { NANOPLOT as NANOPLOT_RAW                              } from '../../mo
 include { NANOPLOT as NANOPLOT_FILTERED                         } from '../../modules/nf-core/nanoplot/main'
 include { NANOLYSE                                              } from '../../modules/nf-core/nanolyse/main'
 include { PORECHOP_ABI                                          } from '../../modules/nf-core/porechop/abi/main'
-include { FILTLONG                                              } from '../../modules/local/filtlong'
-
+include { FILTLONG                                              } from '../../modules/nf-core/filtlong'
 
 workflow LR_PREPROCESSING {
     take:
@@ -57,7 +56,7 @@ workflow LR_PREPROCESSING {
         ch_short_and_long_reads = ch_long_reads
             .map { meta, lr -> [ meta.id, meta, lr ] }
             .join(ch_short_reads_tmp, by: 0)
-            .map { id, meta_lr, lr, meta_sr, sr -> [ meta_lr, lr, sr[0], sr[1] ] }  // should not occur for single-end, since SPAdes (hybrid) does not support single-end
+            .map { id, meta_lr, lr, meta_sr, sr -> [ meta_lr, sr, lr ] }  // should not occur for single-end, since SPAdes (hybrid) does not support single-end
 
         FILTLONG (
             ch_short_and_long_reads
@@ -68,9 +67,10 @@ workflow LR_PREPROCESSING {
         NANOPLOT_FILTERED (
             ch_long_reads
         )
+
+        ch_versions = ch_versions.mix(NANOPLOT_FILTERED.out.versions.first())
     }
 
-    ch_versions = Channel.empty()
     emit:
     long_reads     = ch_long_reads
     versions    = ch_versions