Merge pull request #191 from tfalkarkea/issue-168-deal-properly-with-…

…download-of-data Issue 168 deal properly with download of data
nf-core · Oct 11, 2023 · 26d91c7 · 26d91c7
2 parents 11ec34c + cdde51d
commit 26d91c7
Show file tree

Hide file tree

Showing 6 changed files with 33 additions and 13 deletions.
diff --git a/docs/usage.md b/docs/usage.md
@@ -129,10 +129,14 @@ These options are:
 
 - [kofamscan](https://github.com/takaram/kofam_scan) (`--kofam_dir`)
 
+- [EUKulele](https://github.com/AlexanderLabWHOI/EUKulele) (`--eukulele_dbpath`)
+
 All the options can run in the same time (e.g. `nextflow run main.nf -profile test,docker --eggnog --hmmdir hmms/ --rundbcan`) but each program has its own options that you will need to read carefully before running the pipeline.
 You can find more information about the different options in the [parameters page](https://nf-co.re/metatdenovo/parameters).
 For details about individual programs used, see their respective home pages.
 
+If an Eggnog, kofam, or EUKulele database is already available, they can be specified with the above commands to skip the automatic download that the pipeline performs.
+
 If you don't want run eggNOG-mapper, you will need to add the flag `--skip_eggnog`, otherwise metatdenovo will run the program automatically.
 
 ## Example pipeline command with some common features

diff --git a/nextflow.config b/nextflow.config
@@ -59,7 +59,7 @@ params {
 
     // KOfamscan options
     skip_kofamscan              = false
-    kofam_dir                   = './kofam'
+    kofam_dir                   = './kofam/'
 
     // CAT
     cat                         = false
@@ -71,7 +71,7 @@ params {
     // Eukulele options
     eukulele_db                 = null
     skip_eukulele               = false
-    eukulele_dbpath             = './eukulele'
+    eukulele_dbpath             = './eukulele/'
     eukulele_method             = 'mets'
     // MultiQC options
     multiqc_config             = null
@@ -98,7 +98,7 @@ params {
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
     config_profile_contact     = null
     config_profile_url         = null
-    
+
 
     // Max resource options
     // Defaults only, expecting to be overwritten

diff --git a/subworkflows/local/eggnog.nf b/subworkflows/local/eggnog.nf
@@ -17,7 +17,7 @@ workflow EGGNOG {
 
         String directoryName = eggnog_dbpath
         File directory       = new File(directoryName)
-        String eggnogDB      = eggnog_dbpath + "eggnog.db"
+        String eggnogDB      = eggnog_dbpath + "/eggnog.db"
         File eggnogfile      = new File(eggnogDB)
 
         if ( ! directory.exists() ) {

diff --git a/subworkflows/local/eukulele.nf b/subworkflows/local/eukulele.nf
@@ -9,6 +9,7 @@ include { SUM_TAXONOMY                      } from '../../modules/local/sum_taxo
 workflow SUB_EUKULELE {
 
     take:
+
         eukulele // Channel: val(meta), path(fasta), val(database), path(directory) 
         feature_counts
 

diff --git a/subworkflows/local/kofamscan.nf b/subworkflows/local/kofamscan.nf
@@ -15,12 +15,30 @@ workflow KOFAMSCAN {
 
     main:
         ch_versions = Channel.empty()
-
-        KOFAMSCAN_DOWNLOAD ( kofam_dir )
 
-        KOFAMSCAN_SCAN( kofamscan, KOFAMSCAN_DOWNLOAD.out.ko_list, KOFAMSCAN_DOWNLOAD.out.koprofiles )
+        String directoryName = kofam_dir
+        File directory       = new File(directoryName)
+        String kofamdb       = directoryName + "/ko_list"
+        File kolistfile      = new File(kofamdb)
+
+        if ( ! directory.exists() ) {
+            directory.mkdir()
+        }
+
+        if ( ! kolistfile.exists() ) {
+            KOFAMSCAN_DOWNLOAD ( kofam_dir )
+            ch_dbpath   = KOFAMSCAN_DOWNLOAD.out.ko_list
+            ch_profiles = KOFAMSCAN_DOWNLOAD.out.koprofiles
+
+            ch_versions = ch_versions.mix ( KOFAMSCAN_DOWNLOAD.out.versions )
+        } else {
+            ch_dbpath   = Channel.fromPath(kolistfile)
+            ch_profiles = Channel.fromPath(kofam_dir + "/profiles")
+        }
+
+        KOFAMSCAN_SCAN( kofamscan, ch_dbpath, ch_profiles )
         ch_versions = ch_versions.mix(KOFAMSCAN_SCAN.out.versions)
-        
+
         SUM_KOFAMSCAN( KOFAMSCAN_SCAN.out.kout, fcs )
 
 

diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf
@@ -287,7 +287,7 @@ workflow METATDENOVO {
                 ch_se_reads_to_assembly = ch_interleaved_se.map { meta, fastq -> fastq }
                 ch_pe_reads_to_assembly = Channel.empty()
             }
-        } 
+        }
         else if ( params.bbnorm ) {
             BBMAP_BBNORM(ch_interleaved.collect { meta, fastq -> fastq }.map {[ [id:'all_samples', single_end:true], it ] } )
             ch_pe_reads_to_assembly = BBMAP_BBNORM.out.fastq.map { it[1] }
@@ -459,12 +459,10 @@ workflow METATDENOVO {
     // SUBWORKFLOW: run kofamscan on the ORF-called amino acid sequences
     //
     if( !params.skip_kofamscan ) {
-        File kofam_dir = new File(params.kofam_dir)
-        if ( ! kofam_dir.exists() ) { kofam_dir.mkdir() }
         ch_aa
             .map { [ it[0], it[1] ] }
             .set { ch_kofamscan }
-        KOFAMSCAN( ch_kofamscan, Channel.fromPath(params.kofam_dir), ch_fcs_for_summary)
+        KOFAMSCAN( ch_kofamscan, params.kofam_dir, ch_fcs_for_summary)
         ch_versions = ch_versions.mix(KOFAMSCAN.out.versions)
         ch_kofamscan_summary = KOFAMSCAN.out.kofamscan_summary.collect().map { it[1] }
         ch_merge_tables
@@ -474,7 +472,6 @@ workflow METATDENOVO {
         ch_merge_tables
             .map { [ it[0], it[1], [] ] }
             .set { ch_merge_tables }
-
     }
 
     // set up contig channel to use in CAT and TransRate