Add config and help for lofreq call

src/lofreq/call/config.vsh.yaml

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+functionality:
+  name: lofreq_call
+  description: |
+    Call variants from a BAM file.
+
+    LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.
+
+    LoFreq* can run on almost any type of aligned sequencing data (e.g. Illumina, IonTorrent or Pacbio) since no machine- or sequencing-technology dependent thresholds are used. It automatically adapts to changes in coverage and sequencing quality and can therefore be applied to a variety of data-sets e.g. viral/quasispecies, bacterial, metagenomics or somatic data.
+
+    LoFreq* is very sensitive; most notably, it is able to predict variants below the average base-call quality (i.e. sequencing error rate). Each variant call is assigned a p-value which allows for rigorous false positive control. Even though it uses no approximations or heuristics, it is very efficient due to several runtime optimizations and also provides a (pseudo-)parallel implementation. LoFreq* is generic and fast enough to be applied to high-coverage data and large genomes. On a single processor it takes a minute to analyze Dengue genome sequencing data with nearly 4000X coverage, roughly one hour to call SNVs on a 600X coverage E.coli genome and also roughly an hour to run on a 100X coverage human exome dataset.
+  info:
+    keywords: [ "variant calling", "low frequancy variant calling", "lofreq", "lofreq/call"]
+    homepage: https://csb5.github.io/lofreq/
+    documentation: https://csb5.github.io/lofreq/commands/
+    reference: doi:10.1093/nar/gks918
+    license: "MIT"
+  requirements:
+    commands: [ lofreq ]
+  argument_groups:
+    - name: Inputs
+      arguments:
+        - name: --input
+          type: file
+          description: |
+            Input BAM file.
+          required: true
+          example: "normal.bam"
+    - name: Outputs
+      arguments:
+        - name: --output
+          alternatives: -o
+          type: file
+          description: |
+            Vcf output file [- = stdout].
+          required: true
+          direction: output
+          example: "output.vcf"
+    - name: Arguments
+      arguments:
+        - name: --ref
+          alternatives: -f
+          type: file
+          description: |
+            Indexed reference fasta file (gzip supported) [null].
+          required: false
+          example: "reference.fasta"
+        - name: --region
+          alternatives: -r
+          type: string
+          description: |
+            Limit calls to this region (chrom:start-end) [null].
+          required: false
+          example: "chr1:1000-2000"
+        - name: --bed
+          alternatives: -l
+          type: file
+          description: |
+            List of positions (chr pos) or regions (BED) [null].
+          required: false
+          example: "regions.bed"
+        - name: --min_bq
+          alternatives: -q
+          type: integer
+          description: |
+            Skip any base with baseQ smaller than INT [6].
+          required: false
+          example: 6
+        - name: --min_alt_bq
+          alternatives: -Q
+          type: integer
+          description: |
+            Skip alternate bases with baseQ smaller than INT [6].
+          required: false
+          example: 6
+        - name: --def_alt_bq
+          alternatives: -R
+          type: integer
+          description: |
+            Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0].
+          required: false
+          example: 0
+        - name: --min_jq
+          alternatives: -j
+          type: integer
+          description: |
+            Skip any base with joinedQ smaller than INT [0].
+          example: 0
+        - name: --min_alt_jq
+          alternatives: -J
+          type: integer
+          description: |
+            Skip alternate bases with joinedQ smaller than INT [0].
+          required: false
+          example: 0
+        - name: --def_alt_jq
+          alternatives: -K
+          type: integer
+          description: |
+            Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0].
+          required: false
+          example: 0
+        - name: --no_baq
+          alternatives: -B
+          type: boolean_true
+          description: |
+            Disable use of base-alignment quality (BAQ).
+        - name: --no_idaq
+          alternatives: -A
+          type: boolean_true
+          description: |
+            Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging).
+        - name: --del_baq
+          alternatives: -D
+          type: boolean_true
+          description: |
+            Delete pre-existing BAQ values, i.e. compute even if already present in BAM.
+        - name: --no_ext_baq
+          alternatives: -e
+          type: boolean_true
+          description: |
+            Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag).
+        - name: --min_mq
+          alternatives: -m
+          type: integer
+          description: |
+            Skip reads with mapping quality smaller than INT [0].
+          required: false
+          example: 0
+        - name: --max_mq
+          alternatives: -M
+          type: integer
+          description: |
+            Cap mapping quality at INT [255].
+          required: false
+          example: 255
+        - name: --no_mq
+          alternatives: -N
+          type: boolean_true
+          description: |
+            Don't merge mapping quality in LoFreq's model.
+        - name: --call_indels
+          type: boolean_true
+          description: |
+            Enable indel calls (note: preprocess your file to include indel alignment qualities!).
+        - name: --only_indels
+          type: boolean_true
+          description: |
+            Only call indels; no SNVs.
+        - name: --src_qual
+          alternatives: -s
+          type: boolean_true
+          description: |
+            Enable computation of source quality.
+        - name: --ign_vcf
+          alternatives: -S
+          type: file
+          description: |
+            Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas.
+          required: false
+          multiple: true
+          separator: ","
+          example: "variants.vcf"
+        - name: --def_nm_q
+          alternatives: -T
+          type: integer
+          description: |
+            If >= 0, then replace non-match base qualities with this default value [-1].
+          required: false
+          example: -1
+        - name: --sig
+          alternatives: -a
+          type: double
+          description: |
+            P-Value cutoff / significance level [0.010000]
+          required: false
+          example: 0.01
+        - name: --bonf
+          alternatives: -b
+          type: string
+          description: |
+            Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']
+          required: false
+          example: "dynamic"
+        - name: --min_cov
+          alternatives: -C
+          type: integer
+          description: |
+            Test only positions having at least this coverage [1].
+            (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done).
+          required: false
+          example: 1
+        - name: --max_depth
+          alternatives: -d
+          type: integer
+          description: |
+            Cap coverage at this depth [1000000].
+          required: false
+          example: 1000000
+        - name: --illumina_13
+          type: boolean_true
+          description: |
+            Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded.
+        - name: --use_orphan
+          type: boolean_true
+          description: |
+            Count anomalous read pairs (i.e. where mate is not aligned properly).
+        - name: --plp_summary_only
+          type: boolean_true
+          description: |
+            No variant calling. Just output pileup summary per column.
+        - name: --no_default_filter
+          type: boolean_true
+          description: |
+            Don't run default 'lofreq filter' automatically after calling variants.
+        - name: --force_overwrite
+          type: boolean_true
+          description: |
+            Overwrite any existing output.
+        - name: --verbose
+          type: boolean_true
+          description: |
+            Be verbose.
+        - name: --debug
+          type: boolean_true
+          description: |
+            Enable debugging.
+  resources:
+    - type: bash_script
+      path: script.sh
+platforms:
+  - type: docker
+    image: quay.io/biocontainers/lofreq:2.1.5--py38h794fc9e_10
+    setup:
+      - type: docker
+        run: |
+          version=$(lofreq version | grep 'version' | sed 's/version: //') && \
+          echo "lofreq: $version" > /var/software_versions.txt
+  - type: nextflow
+

src/lofreq/call/help.txt

@@ -0,0 +1,49 @@
+lofreq call: call variants from BAM file
+
+Usage: lofreq call [options] in.bam
+
+Options:
+- Reference:
+       -f | --ref FILE              Indexed reference fasta file (gzip supported) [null]
+- Output:
+       -o | --out FILE              Vcf output file [- = stdout]
+- Regions:
+       -r | --region STR            Limit calls to this region (chrom:start-end) [null]
+       -l | --bed FILE              List of positions (chr pos) or regions (BED) [null]
+- Base-call quality:
+       -q | --min-bq INT            Skip any base with baseQ smaller than INT [6]
+       -Q | --min-alt-bq INT        Skip alternate bases with baseQ smaller than INT [6]
+       -R | --def-alt-bq INT        Overwrite baseQs of alternate bases (that passed bq filter) with this value (-1: use median ref-bq; 0: keep) [0]
+       -j | --min-jq INT            Skip any base with joinedQ smaller than INT [0]
+       -J | --min-alt-jq INT        Skip alternate bases with joinedQ smaller than INT [0]
+       -K | --def-alt-jq INT        Overwrite joinedQs of alternate bases (that passed jq filter) with this value (-1: use median ref-bq; 0: keep) [0]
+- Base-alignment (BAQ) and indel-aligment (IDAQ) qualities:
+       -B | --no-baq                Disable use of base-alignment quality (BAQ)
+       -A | --no-idaq               Don't use IDAQ values (NOT recommended under ANY circumstances other than debugging)
+       -D | --del-baq               Delete pre-existing BAQ values, i.e. compute even if already present in BAM
+       -e | --no-ext-baq            Use 'normal' BAQ (samtools default) instead of extended BAQ (both computed on the fly if not already present in lb tag)
+- Mapping quality:
+       -m | --min-mq INT            Skip reads with mapping quality smaller than INT [0]
+       -M | --max-mq INT            Cap mapping quality at INT [255]
+       -N | --no-mq                 Don't merge mapping quality in LoFreq's model
+- Indels:
+            --call-indels           Enable indel calls (note: preprocess your file to include indel alignment qualities!)
+            --only-indels           Only call indels; no SNVs
+- Source quality:
+       -s | --src-qual              Enable computation of source quality
+       -S | --ign-vcf FILE          Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas
+       -T | --def-nm-q INT          If >= 0, then replace non-match base qualities with this default value [-1]
+- P-values:
+       -a | --sig                   P-Value cutoff / significance level [0.010000]
+       -b | --bonf                  Bonferroni factor. 'dynamic' (increase per actually performed test) or INT ['dynamic']
+- Misc.:
+       -C | --min-cov INT           Test only positions having at least this coverage [1]
+                                    (note: without --no-default-filter default filters (incl. coverage) kick in after predictions are done)
+       -d | --max-depth INT         Cap coverage at this depth [1000000]
+            --illumina-1.3          Assume the quality is Illumina-1.3-1.7/ASCII+64 encoded
+            --use-orphan            Count anomalous read pairs (i.e. where mate is not aligned properly)
+            --plp-summary-only      No variant calling. Just output pileup summary per column
+            --no-default-filter     Don't run default 'lofreq filter' automatically after calling variants
+            --force-overwrite       Overwrite any existing output
+            --verbose               Be verbose
+            --debug                 Enable debugging