diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3f0b90c6f19356a604142813749e0f4e2e5e2b35..81be2dbcf9d9ec030b525e6c366cd3e9d59389aa 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,12 @@ that users understand how the changes affect the new version.
version 2.1.0-dev
---------------------------
++ Added parameter_meta sections to the following tools:
+ + htseq
+ + cutadapt
+ + collect-columns
+ + stringtie
+ + fastqc
+ Updated star default image to 2.7.3a
+ Hisat2 now indexes the resulting BAM file.
+ Samtools index now also works without setting a path for the output
diff --git a/bwa.wdl b/bwa.wdl
index f821b9173ed1a6f64aaf854a0e885f4822dca617..6623899134615340dffd9d2def09e3e4379c9b88 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -104,7 +104,7 @@ task Kit {
category: "required"
}
outputPrefix: {
- description: "The prefix of the output files, including any parent directories",
+ description: "The prefix of the output files, including any parent directories.",
category: "required"
}
readgroup: {
@@ -128,7 +128,7 @@ task Kit {
category: "advanced"
}
dockerImage: {
- description: "The docker image used for this task. Changing this may result in errors which the developers may chose not to address.",
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"
}
diff --git a/collect-columns.wdl b/collect-columns.wdl
index fce0cfa9a9ebdb8232057222858e589be607e521..263e317dc4c36b413ad5643c77c49ec17926e7e5 100644
--- a/collect-columns.wdl
+++ b/collect-columns.wdl
@@ -42,4 +42,51 @@ task CollectColumns {
memory: "~{memoryGb}G"
docker: dockerImage
}
+
+ parameter_meta {
+ inputTables: {
+ description: "The tables from which columns should be taken.",
+ category: "required"
+ }
+ outputPath: {
+ description: "The path to which the output should be written.",
+ category: "required"
+ }
+ featureColumn: {
+ description: "Equivalent to the -f option of collect-columns.",
+ category: "common" # Should likely be controlled by the calling workflow
+ }
+ valueColumn: {
+ description: "Equivalent to the -c option of collect-columns.",
+ category: "common" # Should likely be controlled by the calling workflow
+ }
+ separator: {
+ description: "Equivalent to the -s option of collect-columns.",
+ category: "common" # Should likely be controlled by the calling workflow
+ }
+ sampleNames: {
+ description: "Equivalent to the -n option of collect-columns.",
+ category: "common" # Should likely be controlled by the calling workflow
+ }
+ header: {
+ description: "Equivalent to the -H flag of collect-columns.",
+ category: "common"
+ }
+ additionalAttributes: {
+ description: "Equivalent to the -a option of collect-columns.",
+ category: "advanced"
+ }
+ referenceGtf: {
+ description: "Equivalent to the -g option of collect-columns.",
+ category: "advanced"
+ }
+ featureAttribute: {
+ description: "Equivalent to the -F option of collect-columns.",
+ category: "advanced"
+ }
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"
+ }
+ }
}
\ No newline at end of file
diff --git a/cutadapt.wdl b/cutadapt.wdl
index ff2be2f3c8da0c9887fc116414043dc62fb08f08..571bc884a23a3691006dbdc1e9ad6029c24d4a8b 100644
--- a/cutadapt.wdl
+++ b/cutadapt.wdl
@@ -116,7 +116,7 @@ task Cutadapt {
~{true="--no-trim" false="" noTrim} \
~{true="--mask-adapter" false="" maskAdapter} \
~{true="--no-indels" false="" noIndels} \
- ~{true="--trim-n" false="" trimN} \
+ ~{true="--trim-n" false="" trimN} \
~{true="--interleaved" false="" interleaved} \
~{true="--discard-trimmed" false="" discardTrimmed } \
~{true="--colorspace" false="" colorspace} \
@@ -151,4 +151,239 @@ task Cutadapt {
memory: memory
docker: dockerImage
}
+
+ parameter_meta {
+ read1: {
+ description: "The first or single end fastq file to be run through cutadapt.",
+ category: "required"
+ }
+ read2: {
+ description: "An optional second end fastq file to be run through cutadapt.",
+ category: "common"
+ }
+ read1output: {
+ description: "The name of the resulting first or single end fastq file.",
+ category: "common"
+ }
+ read2output: {
+ description: "The name of the resulting second end fastq file.",
+ category: "common"
+ }
+ format: {
+ description: "Equivalent to cutadapt's --format option.",
+ category: "advanced"
+ }
+ adapter: {
+ description: "A list of 3' ligated adapter sequences to be cut from the given first or single end fastq file.",
+ category: "common"
+ }
+ front: {
+ description: "A list of 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
+ category: "advanced"
+ }
+ anywhere: {
+ description: "A list of 3' or 5' ligated adapter sequences to be cut from the given first or single end fastq file.",
+ category: "advanced"
+ }
+ adapterRead2: {
+ description: "A list of 3' ligated adapter sequences to be cut from the given second end fastq file.",
+ category: "common"
+ }
+ frontRead2: {
+ description: "A list of 5' ligated adapter sequences to be cut from the given second end fastq file.",
+ category: "advanced"
+ }
+ anywhereRead2: {
+ description: "A list of 3' or 5' ligated adapter sequences to be cut from the given second end fastq file.",
+ category: "advanced"
+ }
+ interleaved: {
+ description: "Equivalent to cutadapt's --interleaved flag.",
+ category: "advanced"
+ }
+ pairFilter: {
+ description: "Equivalent to cutadapt's --pair-filter option.",
+ category: "advanced"
+ }
+ errorRate: {
+ description: "Equivalent to cutadapt's --error-rate option.",
+ category: "advanced"
+ }
+ noIndels: {
+ description: "Equivalent to cutadapt's --no-indels flag.",
+ category: "advanced"
+ }
+ times: {
+ description: "Equivalent to cutadapt's --times option.",
+ category: "advanced"
+ }
+ overlap: {
+ description: "Equivalent to cutadapt's --overlap option.",
+ category: "advanced"
+ }
+ matchReadWildcards: {
+ description: "Equivalent to cutadapt's --match-read-wildcards flag.",
+ category: "advanced"
+ }
+ noMatchAdapterWildcards: {
+ description: "Equivalent to cutadapt's --no-match-adapter-wildcards flag.",
+ category: "advanced"
+ }
+ noTrim: {
+ description: "Equivalent to cutadapt's --no-trim flag.",
+ category: "advanced"
+ }
+ maskAdapter: {
+ description: "Equivalent to cutadapt's --mask-adapter flag.",
+ category: "advanced"
+ }
+ cut: {
+ description: "Equivalent to cutadapt's --cut option.",
+ category: "advanced"
+ }
+ nextseqTrim: {
+ description: "Equivalent to cutadapt's --nextseq-trim option.",
+ category: "advanced"
+ }
+ qualityCutoff: {
+ description: "Equivalent to cutadapt's --quality-cutoff option.",
+ category: "advanced"
+ }
+ qualityBase: {
+ description: "Equivalent to cutadapt's --quality-base option.",
+ category: "advanced"
+ }
+ length: {
+ description: "Equivalent to cutadapt's --length option.",
+ category: "advanced"
+ }
+ trimN: {
+ description: "Equivalent to cutadapt's --trim-n flag.",
+ category: "advanced"
+ }
+ lengthTag: {
+ description: "Equivalent to cutadapt's --length-tag option.",
+ category: "advanced"
+ }
+ stripSuffix: {
+ description: "Equivalent to cutadapt's --strip-suffix option.",
+ category: "advanced"
+ }
+ prefix: {
+ description: "Equivalent to cutadapt's --prefix option.",
+ category: "advanced"
+ }
+ suffix: {
+ description: "Equivalent to cutadapt's --suffix option.",
+ category: "advanced"
+ }
+ minimumLength: {
+ description: "Equivalent to cutadapt's --minimum-length option.",
+ category: "advanced"
+ }
+ maximumLength: {
+ description: "Equivalent to cutadapt's --maximum-length option.",
+ category: "advanced"
+ }
+ maxN: {
+ description: "Equivalent to cutadapt's --max-n option.",
+ category: "advanced"
+ }
+ discardTrimmed: {
+ description: "Equivalent to cutadapt's --quality-cutoff option.",
+ category: "advanced"
+ }
+ discardUntrimmed: {
+ description: "Equivalent to cutadapt's --discard-untrimmed option.",
+ category: "advanced"
+ }
+ infoFilePath: {
+ description: "Equivalent to cutadapt's --info-file option.",
+ category: "advanced"
+ }
+ restFilePath: {
+ description: "Equivalent to cutadapt's --rest-file option.",
+ category: "advanced"
+ }
+ wildcardFilePath: {
+ description: "Equivalent to cutadapt's --wildcard-file option.",
+ category: "advanced"
+ }
+ tooShortOutputPath: {
+ description: "Equivalent to cutadapt's --too-short-output option.",
+ category: "advanced"
+ }
+ tooLongOutputPath: {
+ description: "Equivalent to cutadapt's --too-long-output option.",
+ category: "advanced"
+ }
+ untrimmedOutputPath: {
+ description: "Equivalent to cutadapt's --untrimmed-output option.",
+ category: "advanced"
+ }
+ tooShortPairedOutputPath: {
+ description: "Equivalent to cutadapt's --too-short-paired-output option.",
+ category: "advanced"
+ }
+ tooLongPairedOutputPath: {
+ description: "Equivalent to cutadapt's --too-long-paired-output option.",
+ category: "advanced"
+ }
+ untrimmedPairedOutputPath: {
+ description: "Equivalent to cutadapt's --untrimmed-paired-output option.",
+ category: "advanced"
+ }
+ colorspace: {
+ description: "Equivalent to cutadapt's --colorspace flag.",
+ category: "advanced"
+ }
+ doubleEncode: {
+ description: "Equivalent to cutadapt's --double-encode flag.",
+ category: "advanced"
+ }
+ trimPrimer: {
+ description: "Equivalent to cutadapt's --trim-primer flag.",
+ category: "advanced"
+ }
+ stripF3: {
+ description: "Equivalent to cutadapt's --strip-f3 flag.",
+ category: "advanced"
+ }
+ maq: {
+ description: "Equivalent to cutadapt's --maq flag.",
+ category: "advanced"
+ }
+ bwa: {
+ description: "Equivalent to cutadapt's --bwa flag.",
+ category: "advanced"
+ }
+ zeroCap: {
+ description: "Equivalent to cutadapt's --zero-cap flag.",
+ category: "advanced"
+ }
+ noZeroCap: {
+ description: "Equivalent to cutadapt's --no-zero-cap flag.",
+ category: "advanced"
+ }
+ reportPath: {
+ description: "The name of the file to write cutadapts's stdout to, this contains some metrics.",
+ category: "common"
+ }
+ Z: {
+ description: "Equivalent to cutadapt's -Z flag.",
+ category: "advanced"
+ }
+ cores: {
+ description: "The number of cores to use.",
+ category: "advanced"
+ }
+ memory: {
+ description: "The amount of memory this job will use.",
+ category: "advanced"
+ }
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"
+ }
+ }
}
diff --git a/fastqc.wdl b/fastqc.wdl
index 4c68cd26b13f4af531e84dc4de2851b3da76bd96..931c153a68c374bc2d0f9f51187c09cd2f5936cf 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -63,6 +63,79 @@ task Fastqc {
cpu: threads
docker: dockerImage
}
+
+ parameter_meta {
+ seqFile: {
+ description: "A fastq file.",
+ category: "required"
+ }
+ outdirPath: {
+ description: "The path to write the output to",
+ catgory: "required"
+ }
+ casava: {
+ description: "Equivalent to fastqc's --casava flag.",
+ category: "advanced"
+ }
+ nano: {
+ description: "Equivalent to fastqc's --nano flag.",
+ category: "advanced"
+ }
+ noFilter: {
+ description: "Equivalent to fastqc's --nofilter flag.",
+ category: "advanced"
+ }
+ extract: {
+ description: "Equivalent to fastqc's --extract flag.",
+ category: "advanced"
+ }
+ nogroup: {
+ description: "Equivalent to fastqc's --nogroup flag.",
+ category: "advanced"
+ }
+ minLength: {
+ description: "Equivalent to fastqc's --min_length option.",
+ category: "advanced"
+ }
+ format: {
+ description: "Equivalent to fastqc's --format option.",
+ category: "advanced"
+ }
+ contaminants: {
+ description: "Equivalent to fastqc's --contaminants option.",
+ category: "advanced"
+ }
+ adapters: {
+ description: "Equivalent to fastqc's --adapters option.",
+ category: "advanced"
+ }
+ limits: {
+ description: "Equivalent to fastqc's --limits option.",
+ category: "advanced"
+ }
+ kmers: {
+ description: "Equivalent to fastqc's --kmers option.",
+ category: "advanced"
+ }
+ dir: {
+ description: "Equivalent to fastqc's --dir option.",
+ category: "advanced"
+ }
+ threads: {
+ description: "The number of cores to use.",
+ category: "advanced"
+ }
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"
+ }
+ }
+
+ meta {
+ WDL_AID: {
+ exclude: ["NoneFile", "NoneArray"]
+ }
+ }
}
task GetConfiguration {
@@ -89,4 +162,11 @@ task GetConfiguration {
memory: "2G" # Needs more than 1 to pull the docker image
docker: dockerImage
}
+
+ parameter_meta {
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"
+ }
+ }
}
diff --git a/htseq.wdl b/htseq.wdl
index d8009a3b5c7fa3ea14fb3f9b5d0dbc83fa12b15f..645396e8061179df2d119d61baef6cac35af1b59 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -39,4 +39,51 @@ task HTSeqCount {
memory: memory
docker: dockerImage
}
+
+ parameter_meta {
+ inputBams: {
+ description: "The input BAM files.",
+ category: "required"
+ }
+ gtfFile: {
+ description: "A GTF/GFF file containing the features of interest.",
+ category: "required"
+ }
+ outputTable: {
+ description: "The path to which the output table should be written.",
+ category: "common"
+ }
+ format: {
+ description: "Equivalent to the -f option of htseq-count.",
+ category: "advanced"
+ }
+ order: {
+ description: "Equivalent to the -r option of htseq-count.",
+ category: "advanced"
+ }
+ stranded: {
+ description: "Equivalent to the -s option of htseq-count.",
+ category: "common"
+ }
+ featureType: {
+ description: "Equivalent to the --type option of htseq-count.",
+ category: "advanced"
+ }
+ idattr: {
+ description: "Equivalent to the --idattr option of htseq-count.",
+ category: "advanced"
+ }
+ additionalAttributes: {
+ description: "Equivalent to the --additional-attr option of htseq-count.",
+ category: "advanced"
+ }
+ memory: {
+ description: "The amount of memory the job requires in GB.",
+ category: "advanced"
+ }
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"
+ }
+ }
}
diff --git a/stringtie.wdl b/stringtie.wdl
index dd267aa5b63236b2328a29b3f1863191ef8b680a..3392d7b21da26942f25fc93fc34327d95575d7ce 100644
--- a/stringtie.wdl
+++ b/stringtie.wdl
@@ -40,6 +40,53 @@ task Stringtie {
memory: memory
docker: dockerImage
}
+
+ parameter_meta {
+ bam: {
+ description: "The input BAM file.",
+ category: "required"
+ }
+ bamIndex: {
+ description: "The input BAM file's index.",
+ category: "required"
+ }
+ referenceGtf: {
+ description: "A reference GTF file to be used as guide.",
+ category: "common"
+ }
+ skipNovelTranscripts: {
+ description: "Whether new transcripts should be assembled or not.",
+ category: "common"
+ }
+ assembledTranscriptsFile: {
+ description: "Where the output of the assembly should be written.",
+ category: "required"
+ }
+ firstStranded: {
+ description: "Equivalent to the --rf flag of stringtie.",
+ category: "required"
+ }
+ secondStranded: {
+ description: "Equivalent to the --fr flag of stringtie.",
+ category: "required"
+ }
+ geneAbundanceFile: {
+ description: "Where the abundance file should be written.",
+ category: "common"
+ }
+ threads: {
+ description: "The number of threads to use.",
+ category: "advanced"
+ }
+ memory: {
+ description: "The amount of memory needed for this task in GB.",
+ category: "advanced"
+ }
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"
+ }
+ }
}
task Merge {
@@ -83,4 +130,55 @@ task Merge {
memory: memory
docker: dockerImage
}
+
+ parameter_meta {
+ gtfFiles: {
+ description: "The GTF files produced by stringtie.",
+ category: "required"
+ }
+ outputGtfPath: {
+ description: "Where the output should be written.",
+ category: "required"
+ }
+ guideGtf: {
+ description: "Equivalent to the -G option of 'stringtie --merge'.",
+ category: "advanced"
+ }
+ minimumLength: {
+ description: "Equivalent to the -m option of 'stringtie --merge'.",
+ category: "advanced"
+ }
+ minimumCoverage: {
+ description: "Equivalent to the -c option of 'stringtie --merge'.",
+ category: "advanced"
+ }
+ minimumFPKM: {
+ description: "Equivalent to the -F option of 'stringtie --merge'.",
+ category: "advanced"
+ }
+ minimumTPM: {
+ description: "Equivalent to the -T option of 'stringtie --merge'.",
+ category: "advanced"
+ }
+ minimumIsoformFraction: {
+ description: "Equivalent to the -f option of 'stringtie --merge'.",
+ category: "advanced"
+ }
+ keepMergedTranscriptsWithRetainedIntrons: {
+ description: "Equivalent to the -i flag of 'stringtie --merge'.",
+ category: "advanced"
+ }
+ label: {
+ description: "Equivalent to the -l option of 'stringtie --merge'.",
+ category: "advanced"
+ }
+ memory: {
+ description: "The amount of memory needed for this task in GB.",
+ category: "advanced"
+ }
+ dockerImage: {
+ description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
+ category: "advanced"
+ }
+ }
}