Verified Commit b686c25d authored by Aurélien Ginolhac's avatar Aurélien Ginolhac 🚴
Browse files

remove featureCounts and deseq2 for now

parent e62b0c4f
......@@ -162,6 +162,15 @@ salloc: Nodes iris-139 are ready for job
(snakemake) aginolhac@iris-139(14:17:23)-> 29:49)(2424900 1N/T/1CN): ~ $
```
### Fetch test datasets
Using the [nextflow datasets](https://github.com/nf-core/test-datasets), clone it using `git`:
```bash
git clone -b --depth 1 chipseq https://github.com/nf-core/test-datasets.git
```
### Dry-run
......
......@@ -139,96 +139,4 @@ rule merge_bool_and_annotatepeaks:
shell:
"paste {input.bool} {input.trim} > {output}"
rule feature_counts:
input:
sam=lambda wc: expand("results/filtered/{sample}.sorted.bam",
sample=get_samples_of_antibody(wc.antibody)),
annotation="results/macs2_merged_expand/{antibody}.consensus_{peak}-peaks.boolean.saf"
output:
multiext("results/feature_counts/{antibody}.consensus_{peak}-peaks",
".featureCounts",
".featureCounts.summary",
".featureCounts.jcounts")
threads:
2
params:
extra="-F SAF -O --fracOverlap 0.2{pe_param}".format(pe_param="" if config["single_end"] else " -p --donotsort")
log:
"logs/feature_counts/{antibody}.consensus_{peak}-peaks.featureCounts.log"
wrapper:
"0.73.0/bio/subread/featurecounts"
rule featurecounts_modified_colnames:
input:
featurecounts="results/feature_counts/{antibody}.consensus_{peak}-peaks.featureCounts",
bam=expand("results/filtered/{sample}.sorted.bam", sample=samples.index),
samples_file=config["samples"]
output:
"results/feature_counts/{antibody}.consensus_{peak}-peaks_modified.featureCounts"
params:
""
log:
"logs/feature_counts/{antibody}.consensus_{peak}-peaks_modified.featureCounts.log"
script:
"../scripts/col_mod_featurecounts.py"
rule featurecounts_deseq2:
input:
"results/feature_counts/{antibody}.consensus_{peak}-peaks_modified.featureCounts"
output:
dds="results/deseq2/dss_rld/{antibody}.consensus_{peak}-peaks.dds.rld.RData",
plot_pca=report("results/deseq2/plots/{antibody}.consensus_{peak}-peaks.pca_plot.pdf",
caption = "../report/plot_deseq2_pca.rst", category = "DESeq2"),
plot_heatmap=report("results/deseq2/plots/{antibody}.consensus_{peak}-peaks.heatmap_plot.pdf",
caption = "../report/plot_deseq2_heatmap.rst", category = "DESeq2"),
pca_data="results/deseq2/pca_vals/{antibody}.consensus_{peak}-peaks.pca.vals.txt",
dist_data="results/deseq2/dists/{antibody}.consensus_{peak}-peaks.sample.dists.txt",
size_factors_rdata="results/deseq2/sizeFactors/{antibody}.consensus_{peak}-peaks.sizeFactors.RData",
size_factors_res="results/deseq2/sizeFactors/{antibody}.consensus_{peak}-peaks.sizeFactors.sizeFactor.txt",
results="results/deseq2/results/{antibody}.consensus_{peak}-peaks.deseq2_results.txt",
# pairwise comparisons of samples across the groups from a particular antibody
FDR_1_perc_res=directory("results/deseq2/FDR/results/FDR_0.01_{antibody}.consensus_{peak}-peaks"),
FDR_5_perc_res=directory("results/deseq2/FDR/results/FDR_0.05_{antibody}.consensus_{peak}-peaks"),
FDR_1_perc_bed=directory("results/deseq2/FDR/bed_files/FDR_0.01_{antibody}.consensus_{peak}-peaks"),
FDR_5_perc_bed=directory("results/deseq2/FDR/bed_files/FDR_0.05_{antibody}.consensus_{peak}-peaks"),
igv_FDR_5_bed="results/IGV/consensus/merged_library.{antibody}.consensus_{peak}-peaks.deseq2.FDR_0.05.igv.txt",
plot_FDR_1_perc_MA=report(
directory("results/deseq2/comparison_plots/MA_plots/FDR_0.01_{antibody}consensus_{peak}-peaks"),
patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.MA-plot_FDR_0.01.pdf"],
caption = "../report/plot_deseq2_FDR_1_perc_MA.rst",
category = "DESeq2"),
plot_FDR_5_perc_MA=report(
directory("results/deseq2/comparison_plots/MA_plots/FDR_0.05_{antibody}consensus_{peak}-peaks"),
patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.MA-plot_FDR_0.05.pdf"],
caption = "../report/plot_deseq2_FDR_5_perc_MA.rst",
category = "DESeq2"),
plot_FDR_1_perc_volcano=report(
directory("results/deseq2/comparison_plots/volcano_plots/FDR_0.01_{antibody}consensus_{peak}-peaks"),
patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.volcano_FDR_0.01.pdf"],
caption = "../report/plot_deseq2_FDR_1_perc_volcano.rst",
category = "DESeq2"),
plot_FDR_5_perc_volcano=report(
directory("results/deseq2/comparison_plots/volcano_plots/FDR_0.05_{antibody}consensus_{peak}-peaks"),
patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.volcano_FDR_0.05.pdf"],
caption = "../report/plot_deseq2_FDR_5_perc_volcano.rst",
category = "DESeq2"),
plot_sample_corr_heatmap=report(
directory("results/deseq2/comparison_plots/correlation_heatmaps_{antibody}consensus_{peak}-peaks"),
patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.correlation_heatmap.pdf"],
caption = "../report/plot_deseq2_sample_corr_heatmap.rst",
category = "DESeq2"),
plot_scatter=report(
directory("results/deseq2/comparison_plots/scatter_plots_{antibody}consensus_{peak}-peaks"),
patterns=["{antibody}.{group_1}_{antibody_1}_{control_1}vs{group_2}_{antibody_2}_{control_2}.scatter_plots.pdf"],
caption = "../report/plot_deseq2_scatter.rst",
category = "DESeq2")
threads:
2
params:
vst = config["params"]["deseq2"]["vst"]
log:
"logs/deseq2/{antibody}.consensus_{peak}-peaks.featureCounts.log"
conda:
"../envs/featurecounts_deseq2.yaml"
script:
"../scripts/featurecounts_deseq2.R"
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