Merge pull request #131 from MartinPippel/hifiasm_update

bump hifiasm version

modules.json

@@ -62,7 +62,7 @@
           },
           "hifiasm": {
             "branch": "master",
-            "git_sha": "aecb06fcdb995ff3e3df7c7a1fd119367d6d1996",
+            "git_sha": "daa15d5226111e10ca95c0d4a85fa6bd11a08a01",
             "installed_by": ["modules"]
           },
           "kraken2/kraken2": {

modules/nf-core/hifiasm/environment.yml

@@ -1,7 +1,5 @@
-name: hifiasm
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - bioconda::hifiasm=0.19.8
+  - bioconda::hifiasm=0.20.0

modules/nf-core/hifiasm/main.nf

@@ -4,15 +4,13 @@ process HIFIASM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hifiasm:0.19.8--h43eeafb_0' :
-        'biocontainers/hifiasm:0.19.8--h43eeafb_0' }"
+        'https://depot.galaxyproject.org/singularity/hifiasm:0.20.0--h43eeafb_0' :
+        'biocontainers/hifiasm:0.20.0--h43eeafb_0' }"
 
     input:
-    tuple val(meta), path(reads)
-    path  paternal_kmer_dump
-    path  maternal_kmer_dump
-    path  hic_read1
-    path  hic_read2
+    tuple val(meta) , path(reads)
+    tuple val(meta1), path(paternal_kmer_dump), path(maternal_kmer_dump)
+    tuple val(meta2), path(hic_read1)         , path(hic_read2)
 
     output:
     tuple val(meta), path("*.r_utg.gfa")       , emit: raw_unitigs

modules/nf-core/hifiasm/meta.yml

@@ -15,85 +15,160 @@ tools:
       tool_dev_url: https://github.com/chhylp123/hifiasm
       doi: "10.1038/s41592-020-01056-5"
       licence: ["MIT"]
+      identifier: biotools:hifiasm
 input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: FASTQ file with PacBio HiFi reads
-      pattern: "*.{fastq}"
-  - paternal_kmer_dump:
-      type: file
-      description: Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
-  - maternal_kmer_dump:
-      type: file
-      description: Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension.
-  - use_parental_kmers:
-      type: boolean
-      description: A flag (true or false) signalling if the module should use the paternal and maternal kmer dumps.
-  - hic_read1:
-      type: file
-      description: Hi-C data Forward reads.
-  - hic_read2:
-      type: file
-      description: Hi-C data Reverse reads.
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: FASTQ file with PacBio HiFi reads
+        pattern: "*.{fastq}"
+  - - meta1:
+        type: map
+        description: |
+          Groovy Map containing information about parental kmers.
+    - paternal_kmer_dump:
+        type: file
+        description: Yak kmer dump file for paternal reads (can be used for haplotype
+          resolution). It can have an arbitrary extension.
+    - maternal_kmer_dump:
+        type: file
+        description: Yak kmer dump file for maternal reads (can be used for haplotype
+          resolution). It can have an arbitrary extension.
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing information about Hi-C reads
+    - hic_read1:
+        type: file
+        description: Hi-C data Forward reads.
+    - hic_read2:
+        type: file
+        description: Hi-C data Reverse reads.
 output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - versions:
-      type: file
-      description: File containing software versions
-      pattern: "versions.yml"
   - raw_unitigs:
-      type: file
-      description: Raw unitigs
-      pattern: "*.r_utg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.r_utg.gfa":
+          type: file
+          description: Raw unitigs
+          pattern: "*.r_utg.gfa"
+  - corrected_reads:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.ec.bin":
+          type: file
+          description: Corrected reads
+          pattern: "*.ec.bin"
+  - source_overlaps:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.ovlp.source.bin":
+          type: file
+          description: Source overlaps
+          pattern: "*.ovlp.source.bin"
+  - reverse_overlaps:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.ovlp.reverse.bin":
+          type: file
+          description: Reverse overlaps
+          pattern: "*.ovlp.reverse.bin"
+  - processed_contigs:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.bp.p_ctg.gfa":
+          type: file
+          description: Processed contigs
+          pattern: "*.bp.p_ctg.gfa"
   - processed_unitigs:
-      type: file
-      description: Processed unitigs
-      pattern: "*.p_utg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.p_utg.gfa":
+          type: file
+          description: Processed unitigs
+          pattern: "*.p_utg.gfa"
   - primary_contigs:
-      type: file
-      description: Primary contigs
-      pattern: "*.asm.p_ctg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.asm.p_ctg.gfa":
+          type: file
+          description: Primary contigs
+          pattern: "*.asm.p_ctg.gfa"
   - alternate_contigs:
-      type: file
-      description: Alternative contigs
-      pattern: "*.asm.a_ctg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.asm.a_ctg.gfa":
+          type: file
+          description: Alternative contigs
+          pattern: "*.asm.a_ctg.gfa"
   - paternal_contigs:
-      type: file
-      description: Paternal contigs
-      pattern: "*.hap1.p_ctg.gfa"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.hap1.p_ctg.gfa":
+          type: file
+          description: Paternal contigs
+          pattern: "*.hap1.p_ctg.gfa"
   - maternal_contigs:
-      type: file
-      description: Maternal contigs
-      pattern: "*.hap2.p_ctg.gfa"
-  - corrected_reads:
-      type: file
-      description: Corrected reads
-      pattern: "*.ec.bin"
-  - source_overlaps:
-      type: file
-      description: Source overlaps
-      pattern: "*.ovlp.source.bin"
-  - reverse_overlaps:
-      type: file
-      description: Reverse overlaps
-      pattern: "*.ovlp.reverse.bin"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.hap2.p_ctg.gfa":
+          type: file
+          description: Maternal contigs
+          pattern: "*.hap2.p_ctg.gfa"
   - log:
-      type: file
-      description: Stderr log
-      pattern: "*.log"
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "*.log":
+          type: file
+          description: Stderr log
+          pattern: "*.log"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 authors:
   - "@sidorov-si"
   - "@scorreard"
   - "@mbeavitt"
+  - "@schmytzi"
 maintainers:
   - "@sidorov-si"
   - "@scorreard"