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mappers.config
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/*
Specs of mapping/alignment tools to be used
Required fields are:
* tool (name),
* version,
* container,
* index i.e. inline indexing script template or indexing template file name
or set to true if if indexing template file is templates/${index}/${tool}.sh
* at least one mapping script template: dna2dna, rna2dna, dna2dna
i.e. inline mapping script or template file name or true if template is ${mode}/${tool}.sh
Script templates embedded in config must be wrapped in single '
(or tripple single ''') quotes to avoid premature evaluation of embeded variables.
Variable used in templates are Nextflow, not bash variables, for example, variable ${ref}
in indexing templates gets replaced with path to appropriate FASTA file.
The template should only include params essential for execution,
fine tuning params are defined separately in mapping_params.config, allowing exploration
of parameter space without changes to the core template.
*/
params {
mappersDefinitions = [
// [
// tool: 'bbmap',
// version: '38.49',
// container: 'rsuchecki/bbmap:38.44_fae5e1e07240e69896dbf7095872fb6fea43d045',
// // index: 'echo bbmap ref=${ref} Xmx=${task.memory.toMega()}M', //
// // not_allowed: 'trip over that!',
// // dna2dna: true //either (triple) single quoted string or true if template dna2dna/${tool}_align.sh is to be used
// index: true, // or explicit 'whatever.sh' under templates/index,
// dna2dna: true, //or explicit 'whatever.sh' under templates/dna2dna,
// rna2rna: true,
// ],
[
tool: 'bbmap',
version: '38.49',
versionCall: 'bbmap.sh version 2>&1 | awk \'/BBMap version/ {print $3}\'',
container: 'rsuchecki/bbmap:38.49_9e975d9bc6a657bc4306f4475be393b9fbe8e3fb',
index: 'bbmap.sh ref=${ref} Xmx=${task.memory.toMega()}M',
dna2dna: true,
rna2rna: true
],
[
tool: 'bbmap',
version: '38.86',
versionCall: 'bbmap.sh version 2>&1 | awk \'/BBMap version/ {print $3}\'',
container: 'quay.io/biocontainers/bbmap:38.86--h1296035_0',
index: 'bbmap.sh ref=${ref} Xmx=${task.memory.toMega()}M',
dna2dna: true,
rna2rna: true
],
[
tool: 'biokanga',
version: '4.3.11',
versionCall: 'biokanga align --version | cut -f4 -d" "',
container: 'rsuchecki/biokanga:4.3.11',
index: 'biokanga index --threads ${task.cpus} -i ${ref} -o ${ref}.sfx --ref ${ref}',
dna2dna: true,
rna2rna: true,
],
[
tool: 'biokanga',
version: '4.4.2',
versionCall: 'biokanga align --version | cut -f4 -d" "',
container: 'csirocropinformatics/biokanga:4.4.2_57f94e3e831cc2290cd86059b4d23dea22228262',
index: true, //or index: 'biokanga index --threads ${task.cpus} -i ${ref} -o ${ref}.sfx --ref ${ref}',
dna2dna: true,
rna2rna: true,
// dna2dna:
// '''
// biokanga align \
// --sfx ${ref}.sfx \
// --in ${reads[0]} \
// --pair ${reads[1]} \
// --out out.bam \
// --threads ${task.cpus} \
// ${ALIGN_PARAMS}
// '''
// --threads ${task.cpus} \
// ${ALIGN_PARAMS}
// '''
],
[
tool: 'bowtie2',
version: '2.3.5',
versionCall: 'bowtie2 --version | awk \'/bowtie2-align-s version.*$/{print $3}\'',
container: 'rsuchecki/bowtie2:2.3.5_cf1abfa200bdeb2d1c3095be1e8ad99142121b45',
index: true,
dna2dna: true,
rna2rna: true,
],
[
tool: 'bwa',
version: '0.7.17-r1188',
versionCall: 'bwa 2>&1 | awk \'/Version.*$/{print $2}\'',
container: 'rsuchecki/bwa:0.7.17_77b3d455e0e4009e6f55b00fe927308c310d74a6',
index: true,
dna2dna: true,
rna2rna: true,
],
[
tool: 'dart',
versionCall: 'dart -v | awk \'{print $2}\'',
version: 'v1.3.5',
container: 'rsuchecki/dart:1.3.5_a2af064d7ed5df1f16e31ea46645793b356a7758',
index: true,
rna2dna: true,
],
[
tool: 'gsnap',
versionCall: 'gsnap --version 2>&1 | awk \'/GSNAP version.*/{print $3}\'',
version: '2019-03-15',
container: 'rsuchecki/gmap-gsnap:2019-03-15_af7b4bf0f03952c583ba30657f2aca90f8a8783a',
index: true,
rna2dna: true,
],
[
tool: 'hisat2',
version: '2.1.0',
versionCall: 'hisat2 --version | head -1 | cut -f3 -d" "',
container: 'rsuchecki/hisat2:2.1.0_4cb1d4007322767b562e98f69179e8ebf6d31fb1',
index: true,
rna2dna: true,
],
[
tool: 'kallisto',
version: '0.46.0',
versionCall: 'kallisto version | cut -f3 -d" "',
container: 'rsuchecki/kallisto:0.46.0_fe13871790208317a506f0a4f7c3a134cb48f0b4',
index: true,
rna2rna: true,
],
[
tool: 'kart',
version: 'v2.5.5',
versionCall: 'kart -v | cut -f2 -d" "',
container: 'quay.io/biocontainers/kart:2.5.5--h7a5e187_0',
index: 'bwt_index ${ref} ${ref}',
dna2dna: 'kart -i ${ref} -f ${reads[0]} -f2 ${reads[1]} -t ${task.cpus} -bo out.bam',
],
[
tool: 'minimap2',
version: '2.17-r941',
versionCall: 'minimap2 --version',
container: 'rsuchecki/minimap2:2.17-r941_8e7b9a0a29bae17c56801fd4abd1b3d78655f299',
index: true,
dna2dna: true,
rna2rna: true,
],
// [
// tool: 'rapmap', //in lieu of salmon container = 'quay.io/biocontainers/salmon:0.14.1--h86b0361_1'
// version: '0.6.0',
// container: 'rsuchecki/rapmap:0.6.0_ea41639d1009f7bf77a0ccc9c777c8090009711f',
// index: true,
// rna2rna: true,
// ],
[
tool: 'star',
version: '2.7.0f',
versionCall: 'STAR --version',
container: 'rsuchecki/star-aligner:2.7.0f_c5dc08f157c803fec027679c00759359c9c8a814',
index: true,
rna2dna: true,
],
[
tool: 'star',
version: '2.7.5a',
versionCall: 'STAR --version',
container: 'quay.io/biocontainers/star:2.7.5a--0',
index: true,
rna2dna: true,
],
// [
// tool: 'subread',
// version: '1.6.4',
// container: 'rsuchecki/subread:1.6.4_6c100baea58da10b0505153e26b92f3a2ad1f8b0',
// index: true,
// rna2dna: true,
// ],
[
tool: 'yara',
version: '1.0.2',
versionCall: 'yara_mapper --version | head -1 | cut -f3 -d" "',
container: 'quay.io/biocontainers/yara:1.0.2--2',
index: 'yara_indexer ${ref} --output-prefix ${ref}.index',
dna2dna: 'yara_mapper ${ref}.index ${reads[0]} ${reads[1]} --output-file out.bam --threads ${task.cpus}',
],
// [
// tool: '',
// version: '',
// container: '',
// index: true,
// dna2dna: true,
// rna2rna: true,
// ],
// [
// tool: '',
// version: '',
// container: '',
// index: true,
// dna2dna: true,
// rna2rna: true,
// ],
]
}