Merge branch 'master' into renovate/biocontainers-cooler-0.x

Author: LouisLeNezet

.github/skip_nf_test.json

@@ -71,7 +71,6 @@
         "modules/nf-core/purgedups/calcuts",
         "modules/nf-core/purgedups/getseqs",
         "modules/nf-core/purgedups/purgedups",
-        "modules/nf-core/quartonotebook",
         "modules/nf-core/scimap/mcmicro",
         "modules/nf-core/scimap/spatiallda",
         "modules/nf-core/sentieon/bwaindex",

modules/nf-core/abacas/meta.yml

@@ -55,7 +55,8 @@ output:
         '*.abacas.tab', '*.abacas.unused.contigs.out',
         '*.abacas.MULTIFASTA.fa' ]
       pattern: "${prefix}.*"
-      ontologies: []
+      ontologies:
+        - edam: "http://edamontology.org/format_3750" # YAML
 - versions:
   - versions.yml:
       type: file

modules/nf-core/abricate/run/meta.yml

@@ -22,6 +22,10 @@ input:
         type: file
         description: FASTA, GenBank or EMBL formatted file
         pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
+        ontologies:
+          - edam: 'http://edamontology.org/format_1929' # FASTA
+          - edam: 'http://edamontology.org/format_1936' # GenBank
+          - edam: 'http://edamontology.org/format_2204' # EMBL format
   - - databasedir:
         type: directory
         description: Optional location of local copy of database files, possibly with
@@ -38,11 +42,15 @@ output:
           type: file
           description: Tab-delimited report of results
           pattern: "*.{txt}"
+          ontologies:
+            - edam: 'http://edamontology.org/format_2330' # Textual format
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies:
+            - edam: 'http://edamontology.org/format_3750' # YAML
 authors:
   - "@rpetit3"
 maintainers:

modules/nf-core/abricate/summary/meta.yml

@@ -22,6 +22,10 @@ input:
         type: file
         description: FASTA, GenBank or EMBL formatted file
         pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929" # FASTA
+          - edam: "http://edamontology.org/format_1936" # GenBank
+          - edam: "http://edamontology.org/format_2204" # EMBL format (XML)
 output:
   - report:
       - meta:
@@ -33,11 +37,15 @@ output:
           type: file
           description: Tab-delimited report of aggregated results
           pattern: "*.{txt}"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330" # Textual format
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies:
+            - edam: "http://edamontology.org/format_3750" # YAML
 authors:
   - "@rpetit3"
 maintainers:

modules/nf-core/abritamr/run/meta.yml

@@ -26,63 +26,87 @@ input:
         type: file
         description: Assembled contigs in FASTA format
         pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1929" # FASTA
 output:
   - matches:
       - meta:
           type: file
           description: Tab-delimited file, with a row per sequence, and columns representing
             functional drug classes
           pattern: "*.summary_matches.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
       - "*.summary_matches.txt":
           type: file
           description: Tab-delimited file, with a row per sequence, and columns representing
             functional drug classes
           pattern: "*.summary_matches.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
   - partials:
       - meta:
           type: file
           description: Tab-delimited file, with a row per sequence, and columns representing
             partial hits to functional drug classes
           pattern: "*.summary_partials.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
       - "*.summary_partials.txt":
           type: file
           description: Tab-delimited file, with a row per sequence, and columns representing
             partial hits to functional drug classes
           pattern: "*.summary_partials.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
   - virulence:
       - meta:
           type: string
           description: Tab-delimited file, with a row per sequence, and columns representing
             AMRFinderPlus virulence gene classification
           pattern: "*.summary_virulence.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
       - "*.summary_virulence.txt":
           type: string
           description: Tab-delimited file, with a row per sequence, and columns representing
             AMRFinderPlus virulence gene classification
           pattern: "*.summary_virulence.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
   - out:
       - meta:
           type: string
           description: raw output from AMRFinder plus (per sequence)
           pattern: "*.amrfinder.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
       - "*.amrfinder.out":
           type: string
           description: raw output from AMRFinder plus (per sequence)
           pattern: "*.amrfinder.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
   - txt:
       - meta:
           type: string
           description: Tab-delimited file, combining non-empty summary files
           pattern: "*.abritamr.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
       - "*.abritamr.txt":
           type: string
           description: Tab-delimited file, combining non-empty summary files
           pattern: "*.abritamr.txt"
+          ontologies: 
+            - edam: "http://edamontology.org/format_2330" # Textual format
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies: 
+            - edam: "http://edamontology.org/format_3750" # YAML
 authors:
   - "@rpetit3"
 maintainers:

modules/nf-core/adapterremoval/meta.yml

@@ -24,12 +24,16 @@ input:
           List of input FastQ files of size 1 and 2 for single-end and paired-end data,
           respectively.
         pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+        ontologies:
+          - edam: "http://edamontology.org/format_1930" # FASTQ
   - - adapterlist:
         type: file
         description: Optional text file containing list of adapters to look for for
           removal with one adapter per line. Otherwise will look for default adapters
           (see AdapterRemoval man page), or can be modified to remove user-specified
           adapters via ext.args.
+        ontologies: 
+          - edam: "http://edamontology.org/format_2330" # Textual format
 output:
   - singles_truncated:
       - meta:
@@ -39,26 +43,34 @@ output:
             'orphaned' reads from merging of paired-end data (i.e., one of the pair
             was lost due to filtering thresholds).
           pattern: "*.truncated.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
       - ${prefix}.truncated.fastq.gz:
           type: file
           description: |
             Adapter trimmed FastQ files of either single-end reads, or singleton
             'orphaned' reads from merging of paired-end data (i.e., one of the pair
             was lost due to filtering thresholds).
           pattern: "*.truncated.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
   - discarded:
       - meta:
           type: file
           description: |
             Adapter trimmed FastQ files of reads that did not pass filtering
             thresholds.
           pattern: "*.discarded.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
       - ${prefix}.discarded.fastq.gz:
           type: file
           description: |
             Adapter trimmed FastQ files of reads that did not pass filtering
             thresholds.
           pattern: "*.discarded.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
   - paired_truncated:
       - meta:
           type: file
@@ -67,64 +79,86 @@ output:
             with their respective R{1,2} pair due to long templates. The respective pair
             is stored in 'pair{1,2}_truncated'.
           pattern: "*.pair{1,2}.truncated.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
       - ${prefix}.pair{1,2}.truncated.fastq.gz:
           type: file
           description: |
             Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge
             with their respective R{1,2} pair due to long templates. The respective pair
             is stored in 'pair{1,2}_truncated'.
           pattern: "*.pair{1,2}.truncated.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
   - collapsed:
       - meta:
           type: file
           description: |
             Collapsed FastQ of paired-end reads that successfully merged with their
             respective R1 pair but were not trimmed.
           pattern: "*.collapsed.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
       - ${prefix}.collapsed.fastq.gz:
           type: file
           description: |
             Collapsed FastQ of paired-end reads that successfully merged with their
             respective R1 pair but were not trimmed.
           pattern: "*.collapsed.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
   - collapsed_truncated:
       - meta:
           type: file
           description: |
             Collapsed FastQ of paired-end reads that successfully merged with their
             respective R1 pair and were trimmed of adapter due to sufficient overlap.
           pattern: "*.collapsed.truncated.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
       - ${prefix}.collapsed.truncated.fastq.gz:
           type: file
           description: |
             Collapsed FastQ of paired-end reads that successfully merged with their
             respective R1 pair and were trimmed of adapter due to sufficient overlap.
           pattern: "*.collapsed.truncated.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
   - paired_interleaved:
       - meta:
           type: file
           description: |
             Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads
           pattern: "*.paired.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
       - ${prefix}.paired.fastq.gz:
           type: file
           description: |
             Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads
           pattern: "*.paired.fastq.gz"
+          ontologies:
+            - edam: "http://edamontology.org/format_1930" # FASTQ
   - settings:
       - meta:
           type: file
           description: AdapterRemoval log file
           pattern: "*.settings"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330" # Textual format
       - "*.settings":
           type: file
           description: AdapterRemoval log file
           pattern: "*.settings"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330" # Textual format
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies:
+            - edam: "http://edamontology.org/format_3750" # YAML
 authors:
   - "@maxibor"
   - "@jfy133"

modules/nf-core/adapterremovalfixprefix/meta.yml

@@ -24,6 +24,8 @@ input:
         type: file
         description: FASTQ file from AdapterRemoval2
         pattern: "*.{fq.gz,fastq.gz}"
+        ontologies: 
+          - edam: "http://edamontology.org/format_1930" # FASTQ
 output:
   - fixed_fastq:
       - meta:
@@ -35,11 +37,15 @@ output:
           type: file
           description: FASTQ file with fixed read prefixes for DeDup
           pattern: "*.{fq.gz}"
+          ontologies: 
+            - edam: "http://edamontology.org/format_1930" # FASTQ
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies: 
+            - edam: "http://edamontology.org/format_3750" # YAML
 authors:
   - "@jfy133"
 maintainers:

modules/nf-core/admixture/meta.yml

@@ -30,17 +30,21 @@ input:
           If you provide ".ped" or ".geno" then you need to provide a ".map" file and
           an empty channel.
         pattern: "*.{bed}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3586" # bed12
     - bim_map:
         type: file
         description: Mandatory accompanying file. One of PLINK ".bim" file or PLINK
           ".map" file. Provide ".bim" if ".bed" is the input. Provide ".map" if ".ped"
           or ".geno" is the input.
         pattern: "*.{bim}"
+        ontologies: []
     - fam:
         type: file
         description: PLINK ".fam" file. Mandatory if you provide ".bed" as input. Replace
           with an empty channel if input is ".ped" or ".geno".
         pattern: "*.{fam}"
+        ontologies: []
   - - K:
         type: integer
         description: Belief of the number of ancestral populations.
@@ -57,6 +61,7 @@ output:
           description: Space-delimited files containing ancestry fractions. The output
             filenames have the number of populations (K) that was assumed for the analysis.
           pattern: "*.{Q}"
+          ontologies: []
   - allele_frequencies:
       - meta:
           type: map
@@ -69,11 +74,14 @@ output:
             inferred ancestral populations. The output filenames have the number of populations
             (K) that was assumed for the analysis.
           pattern: "*.{P}"
+          ontologies: []
   - versions:
       - versions.yml:
           type: file
           description: File containing software versions
           pattern: "versions.yml"
+          ontologies:
+            - edam: "http://edamontology.org/format_3750" # YAML
 authors:
   - "@atrigila"
 maintainers: