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single_end_clip.yaml
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single_end_clip.yaml
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#!/usr/bin/env eCLIP_singleend
### eCLIP_singleend ###
### wf_get_peaks_scatter_se.cwl ###
dataset: SLBP
species: hg19
chrom_sizes:
class: File
path: hg19.chrom.sizes
speciesGenomeDir:
class: Directory
path: hg19_starindex
repeatElementGenomeDir:
class: Directory
path: hg19_repbase_starindex
samples:
-
- ip_read:
name: CLIP_vivo1
read1:
class: File
path: MC_vivo1_IP_S5_L002_R1_001.fastq.gz
adapters:
class: File
path: InvRNA1_adapters.fasta
- input_read:
name: INPUT_vivo1
read1:
class: File
path: MC_vivo1_Input_S1_L002_R1_001.fastq.gz
adapters:
class: File
path: Ril19_adapters.fasta
-
- ip_read:
name: CLIP_vivo2
read1:
class: File
path: MC_vivo2_IP_S6_L002_R1_001.fastq.gz
adapters:
class: File
path: InvRNA1_adapters.fasta
- input_read:
name: INPUT_vivo2
read1:
class: File
path: MC_vivo2_Input_S2_L002_R1_001.fastq.gz
adapters:
class: File
path: Ril19_adapters.fasta
-
- ip_read:
name: CLIP_vitro1
read1:
class: File
path: MC_vitro1_IP_S7_L002_R1_001.fastq.gz
adapters:
class: File
path: InvRNA2_adapters.fasta
- input_read:
name: INPUT_vitro1
read1:
class: File
path: MC_vitro1_Input_S3_L002_R1_001.fastq.gz
adapters:
class: File
path: Ril19_adapters.fasta
-
- ip_read:
name: CLIP_vitro2
read1:
class: File
path: MC_vitro2_IP_S8_L002_R1_001.fastq.gz
adapters:
class: File
path: InvRNA2_adapters.fasta
- input_read:
name: INPUT_vitro2
read1:
class: File
path: MC_vitro2_Input_S4_L002_R1_001.fastq.gz
adapters:
class: File
path: Ril19_adapters.fasta