CI
02c1c9ebea
Build pipeline: viash-hub.biobox.main-7dwhr
Source commit: da414e72c6
Source message: Add star solo component (#62)
* add star solo component
* change arguments from camelCase to snake_case
* get rid of multiple_sep
* drop star_solo component and just add arguments to star_align_reads
* Update src/star/star_align_reads/script.py
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
127 lines
4.2 KiB
Plaintext
127 lines
4.2 KiB
Plaintext
manifest {
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name = 'featurecounts'
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mainScript = 'main.nf'
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nextflowVersion = '!>=20.12.1-edge'
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version = 'main'
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description = 'featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.\n'
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author = 'Sai Nirmayi Yasa'
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}
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process.container = 'nextflow/bash:latest'
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// detect tempdir
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tempDir = java.nio.file.Paths.get(
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System.getenv('NXF_TEMP') ?:
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System.getenv('VIASH_TEMP') ?:
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System.getenv('TEMPDIR') ?:
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System.getenv('TMPDIR') ?:
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'/tmp'
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).toAbsolutePath()
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profiles {
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no_publish {
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process {
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withName: '.*' {
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publishDir = [
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enabled: false
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]
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}
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}
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}
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mount_temp {
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docker.temp = tempDir
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podman.temp = tempDir
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charliecloud.temp = tempDir
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}
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docker {
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docker.enabled = true
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// docker.userEmulation = true
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singularity.enabled = false
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podman.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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}
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singularity {
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singularity.enabled = true
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singularity.autoMounts = true
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docker.enabled = false
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podman.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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}
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podman {
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podman.enabled = true
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docker.enabled = false
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singularity.enabled = false
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shifter.enabled = false
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charliecloud.enabled = false
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}
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shifter {
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shifter.enabled = true
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docker.enabled = false
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singularity.enabled = false
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podman.enabled = false
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charliecloud.enabled = false
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}
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charliecloud {
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charliecloud.enabled = true
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docker.enabled = false
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singularity.enabled = false
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podman.enabled = false
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shifter.enabled = false
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}
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}
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process{
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withLabel: mem1gb { memory = 1000000000.B }
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withLabel: mem2gb { memory = 2000000000.B }
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withLabel: mem5gb { memory = 5000000000.B }
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withLabel: mem10gb { memory = 10000000000.B }
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withLabel: mem20gb { memory = 20000000000.B }
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withLabel: mem50gb { memory = 50000000000.B }
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withLabel: mem100gb { memory = 100000000000.B }
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withLabel: mem200gb { memory = 200000000000.B }
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withLabel: mem500gb { memory = 500000000000.B }
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withLabel: mem1tb { memory = 1000000000000.B }
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withLabel: mem2tb { memory = 2000000000000.B }
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withLabel: mem5tb { memory = 5000000000000.B }
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withLabel: mem10tb { memory = 10000000000000.B }
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withLabel: mem20tb { memory = 20000000000000.B }
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withLabel: mem50tb { memory = 50000000000000.B }
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withLabel: mem100tb { memory = 100000000000000.B }
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withLabel: mem200tb { memory = 200000000000000.B }
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withLabel: mem500tb { memory = 500000000000000.B }
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withLabel: mem1gib { memory = 1073741824.B }
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withLabel: mem2gib { memory = 2147483648.B }
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withLabel: mem4gib { memory = 4294967296.B }
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withLabel: mem8gib { memory = 8589934592.B }
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withLabel: mem16gib { memory = 17179869184.B }
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withLabel: mem32gib { memory = 34359738368.B }
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withLabel: mem64gib { memory = 68719476736.B }
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withLabel: mem128gib { memory = 137438953472.B }
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withLabel: mem256gib { memory = 274877906944.B }
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withLabel: mem512gib { memory = 549755813888.B }
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withLabel: mem1tib { memory = 1099511627776.B }
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withLabel: mem2tib { memory = 2199023255552.B }
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withLabel: mem4tib { memory = 4398046511104.B }
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withLabel: mem8tib { memory = 8796093022208.B }
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withLabel: mem16tib { memory = 17592186044416.B }
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withLabel: mem32tib { memory = 35184372088832.B }
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withLabel: mem64tib { memory = 70368744177664.B }
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withLabel: mem128tib { memory = 140737488355328.B }
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withLabel: mem256tib { memory = 281474976710656.B }
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withLabel: mem512tib { memory = 562949953421312.B }
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withLabel: cpu1 { cpus = 1 }
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withLabel: cpu2 { cpus = 2 }
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withLabel: cpu5 { cpus = 5 }
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withLabel: cpu10 { cpus = 10 }
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withLabel: cpu20 { cpus = 20 }
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withLabel: cpu50 { cpus = 50 }
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withLabel: cpu100 { cpus = 100 }
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withLabel: cpu200 { cpus = 200 }
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withLabel: cpu500 { cpus = 500 }
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withLabel: cpu1000 { cpus = 1000 }
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}
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