Verified Commit c794b217 authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

template for test data and fix trimming PE

parent 4d521fcb
......@@ -223,11 +223,15 @@ snakemake --report
## Expected outputs
With real yeast data:
For the test data:
- the `snakemake` report: `report.html`, download a [copy here](https://xsOdPxjHMEpp3hc:123456@owncloud.lcsb.uni.lu/public.php/webdav/report.html)
- the `multiqc` report: `results/qc/multiqc/multiqc_report.html`, download a [copy here](https://xsOdPxjHMEpp3hc:123456@owncloud.lcsb.uni.lu/public.php/webdav/multiqc.html)
With real yeast data:
- the `snakemake` report: `report.html`, download a [copy here](https://xsOdPxjHMEpp3hc:123456@owncloud.lcsb.uni.lu/public.php/webdav/report_yeast.html)
- the `multiqc` report: `results/qc/multiqc/multiqc_report.html`, download a [copy here](https://xsOdPxjHMEpp3hc:123456@owncloud.lcsb.uni.lu/public.php/webdav/multiqc_yeast.html)
# Credits
......
......@@ -34,7 +34,7 @@ trimming:
params:
# choose "narrow" or "broad" for macs2 callpeak analysis, for documentation and source code please see https://github.com/macs3-project/MACS
peak-analysis: "broad"
peak-analysis: "narrow"
# Number of biological replicates required from a given condition for a peak to contribute to a consensus peak
min-reps-consensus: 1
callpeak:
......@@ -51,10 +51,11 @@ params:
# set to True to use the vst transformation instead of the rlog transformation for the DESeq2 analysis
vst: False
peak-annotation-analysis:
activate: False
activate: True
peak-qc:
activate: True
consensus-peak-analysis:
# when more than one sample
activate: False
# samtools view parameter suggestions (for full parameters, see: https://www.htslib.org/doc/samtools-view.html):
# if duplicates should be removed in this filtering, add "-F 0x0400" to the params
......
sample group batch_effect control antibody
IN_FY4 WT batch1 K4
FY4 WT batch1 IN_FY4 K4
IN_FY4dld3 dld3 batch1 K4
FY4_dld3 dld3 batch1 IN_FY4dld3 K4
\ No newline at end of file
Spt5_IN SptA batch1 Spt
Spt5 SptA batch1 Spt5_IN Spt
\ No newline at end of file
sample group batch_effect control antibody
IN_FY4 WT batch1 K4
FY4 WT batch1 IN_FY4 K4
IN_FY4dld3 dld3 batch1 K4
FY4_dld3 dld3 batch1 IN_FY4dld3 K4
\ No newline at end of file
sample unit fq1 fq2 sra_accession platform
IN_FY4 1 data/2020-08-II/IN_FY4_A_Lasse_S22_R1_001.fastq.gz ILLUMINA
IN_FY4 2 data/2020-08-II/IN_FY4_B_Lasse_S23_R1_001.fastq.gz ILLUMINA
IN_FY4 3 data/2020-08-II/IN_FY4_C_Lasse_S24_R1_001.fastq.gz ILLUMINA
IN_FY4 4 data/2020-08-II/IN_FY4_D_Lasse_S64_R1_001.fastq.gz ILLUMINA
IN_FY4 5 data/2020-08-II/IN_FY4_E_Lasse_S65_R1_001.fastq.gz ILLUMINA
IN_FY4 6 data/2020-08-II/IN_FY4_F_Lasse_S66_R1_001.fastq.gz ILLUMINA
FY4 1 data/2020-08-II/K4_FY4_A_Lasse_S1_R1_001.fastq.gz ILLUMINA
FY4 2 data/2020-08-II/K4_FY4_B_Lasse_S2_R1_001.fastq.gz ILLUMINA
FY4 3 data/2020-08-II/K4_FY4_C_Lasse_S3_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 1 data/2020-08-II/IN_FY4dld3_A_Lasse_S25_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 2 data/2020-08-II/IN_FY4dld3_B_Lasse_S26_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 3 data/2020-08-II/IN_FY4dld3_C_Lasse_S27_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 4 data/2020-08-II/IN_FY4dld3_D_Lasse_S67_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 5 data/2020-08-II/IN_FY4dld3_E_Lasse_S68_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 6 data/2020-08-II/IN_FY4dld3_F_Lasse_S69_R1_001.fastq.gz ILLUMINA
FY4_dld3 1 data/2020-08-II/K4_FY4dld3_A_Lasse_S4_R1_001.fastq.gz ILLUMINA
FY4_dld3 2 data/2020-08-II/K4_FY4dld3_B_Lasse_S5_R1_001.fastq.gz ILLUMINA
FY4_dld3 3 data/2020-08-II/K4_FY4dld3_C_Lasse_S6_R1_001.fastq.gz ILLUMINA
Spt5_IN 1 test-datasets/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz test-datasets/testdata/SRR5204809_Spt5-ChIP_Input1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz ILLUMINA
Spt5_IN 2 test-datasets/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz test-datasets/testdata/SRR5204810_Spt5-ChIP_Input2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz ILLUMINA
Spt5 1 test-datasets/testdata/SRR5204807_Spt5-ChIP_IP1_SacCer_ChIP-Seq_ss100k_R1.fastq.gz test-datasets/testdata/SRR5204807_Spt5-ChIP_IP1_SacCer_ChIP-Seq_ss100k_R2.fastq.gz ILLUMINA
Spt5 2 test-datasets/testdata/SRR5204808_Spt5-ChIP_IP2_SacCer_ChIP-Seq_ss100k_R1.fastq.gz test-datasets/testdata/SRR5204808_Spt5-ChIP_IP2_SacCer_ChIP-Seq_ss100k_R2.fastq.gz ILLUMINA
sample unit fq1 fq2 sra_accession platform
IN_FY4 1 data/2020-08-II/IN_FY4_A_Lasse_S22_R1_001.fastq.gz ILLUMINA
IN_FY4 2 data/2020-08-II/IN_FY4_B_Lasse_S23_R1_001.fastq.gz ILLUMINA
IN_FY4 3 data/2020-08-II/IN_FY4_C_Lasse_S24_R1_001.fastq.gz ILLUMINA
IN_FY4 4 data/2020-08-II/IN_FY4_D_Lasse_S64_R1_001.fastq.gz ILLUMINA
IN_FY4 5 data/2020-08-II/IN_FY4_E_Lasse_S65_R1_001.fastq.gz ILLUMINA
IN_FY4 6 data/2020-08-II/IN_FY4_F_Lasse_S66_R1_001.fastq.gz ILLUMINA
FY4 1 data/2020-08-II/K4_FY4_A_Lasse_S1_R1_001.fastq.gz ILLUMINA
FY4 2 data/2020-08-II/K4_FY4_B_Lasse_S2_R1_001.fastq.gz ILLUMINA
FY4 3 data/2020-08-II/K4_FY4_C_Lasse_S3_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 1 data/2020-08-II/IN_FY4dld3_A_Lasse_S25_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 2 data/2020-08-II/IN_FY4dld3_B_Lasse_S26_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 3 data/2020-08-II/IN_FY4dld3_C_Lasse_S27_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 4 data/2020-08-II/IN_FY4dld3_D_Lasse_S67_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 5 data/2020-08-II/IN_FY4dld3_E_Lasse_S68_R1_001.fastq.gz ILLUMINA
IN_FY4dld3 6 data/2020-08-II/IN_FY4dld3_F_Lasse_S69_R1_001.fastq.gz ILLUMINA
FY4_dld3 1 data/2020-08-II/K4_FY4dld3_A_Lasse_S4_R1_001.fastq.gz ILLUMINA
FY4_dld3 2 data/2020-08-II/K4_FY4dld3_B_Lasse_S5_R1_001.fastq.gz ILLUMINA
FY4_dld3 3 data/2020-08-II/K4_FY4dld3_C_Lasse_S6_R1_001.fastq.gz ILLUMINA
......@@ -216,10 +216,10 @@ def get_multiqc_input(wildcards):
reads = [ "1", "2" ]
if is_single_end(sample, unit):
reads = [ "0" ]
multiqc_input.extend(expand (["logs/trimming/{sample}-{unit}.se.log"],
multiqc_input.extend(expand (["results/trimmed_se/{sample}-{unit}.settings"],
sample = sample, unit = unit))
else:
multiqc_input.extend(expand (["logs/trimming/{sample}-{unit}.pe.log"],
multiqc_input.extend(expand (["results/trimmed_pe/{sample}-{unit}.settings"],
sample = sample, unit = unit))
multiqc_input.extend(
......
......@@ -4,8 +4,8 @@ rule trimming_pe:
# unpack to convert the returned dict to a list
unpack(get_fastq)
output:
fastq1="results/trimmed_pe/{sample}-{unit}.1.fastq.gz",
fastq2="results/trimmed_pe/{sample}-{unit}.2.fastq.gz",
fq1="results/trimmed_pe/{sample}-{unit}.1.fastq.gz",
fq2="results/trimmed_pe/{sample}-{unit}.2.fastq.gz",
single="results/trimmed_pe/{sample}-{unit}.singletons.gz",
discarded="results/trimmed_pe/{sample}-{unit}.discarded.gz",
settings="results/trimmed_pe/{sample}-{unit}.settings"
......
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