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Commit 4f7447ac authored by Dominik Burri's avatar Dominik Burri
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alfa for all samples

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1 merge request!39Alfa qc
Pipeline #10316 passed
Stage: test
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envs/env_alfa.yaml
+ 1
− 0
View file @ 4f7447ac
......@@ -6,3 +6,4 @@ channels:
- defaults
dependencies:
- alfa=1.1.1
- rename=1.600
snakemake/Snakefile
+ 81
− 6
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......@@ -12,11 +12,13 @@ import pandas as pd
samples_table = pd.read_csv(config["samples"], header=0, index_col=0, comment='#', engine='python', sep="\t")
directionality = {"--fr": "fr-firststrand", "--rv": "fr-secondstrand"}
rename_files = {"fr-firststrand": ("STAR_Signal.UniqueMultiple.out.plus.bg",
"STAR_Signal.UniqueMultiple.out.minus.bg"),
"fr-secondstrand": ("STAR_Signal.UniqueMultiple.out.minus.bg",
"STAR_Signal.UniqueMultiple.out.plus.bg")}
rename_files = {"fr-firststrand": ("Signal.UniqueMultiple.out.plus.bg",
"Signal.UniqueMultiple.out.minus.bg"),
"fr-secondstrand": ("Signal.UniqueMultiple.out.minus.bg",
"Signal.UniqueMultiple.out.plus.bg")}
rename_expr = {"fr-firststrand": ("out.plus", "out.minus"),
"fr-secondstrand": ("out.minus", "out.plus")}
localrules: finish
##################################################################################
......@@ -60,7 +62,11 @@ rule finish:
"ALFA_plots.Biotypes.pdf"),
zip,
sample= [i for i in list(samples_table.index.values)],
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)])
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
alfa = os.path.join(
config["output_dir"],
"ALFA",
"ALFA_plots.Biotypes.pdf")
rule create_index_star:
......@@ -193,3 +199,72 @@ rule generate_alfa_index:
-p {threads} \
-o {params.out_dir} &> {log}"
# TODO: add rule that executes ALFA on all samples; should be on the same genome & same orientation
rule alfa_bg_all_samples:
''' Run ALFA from stranded bedgraph files '''
input:
str1 = expand(os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
"{sample}_Signal.UniqueMultiple.str1.out.bg"),
zip,
sample= [i for i in list(samples_table.index.values)],
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
str2 = expand(os.path.join(
config["output_dir"],
"{seqmode}",
"{sample}",
"ALFA",
"{sample}_Signal.UniqueMultiple.str2.out.bg"),
zip,
sample= [i for i in list(samples_table.index.values)],
seqmode= [samples_table.loc[i,"seqmode"] for i in list(samples_table.index.values)]),
gtf = [os.path.join(config["alfa_indexes"], samples_table.loc[sample1, "organism"],
str(samples_table.loc[sample1, "index_size"]), "ALFA", "sorted_genes.stranded.ALFA_index") for sample1 in list(samples_table.index.values)]
output:
biotypes = os.path.join(
config["output_dir"],
"ALFA",
"ALFA_plots.Biotypes.pdf"),
categories = os.path.join(
config["output_dir"],
"ALFA",
"ALFA_plots.Categories.pdf")
params:
str1 = lambda wildcards, input: [os.path.abspath(i) for i in input.str1],
str2 = lambda wildcards, input: [os.path.abspath(i) for i in input.str2],
out_dir = lambda wildcards, output: directory(os.path.dirname(output.biotypes)),
in_file_str1 = lambda wildcards, input: [os.path.basename(inp) for inp in input.str1], # copy files into out_dir and create with expand construct of bg + name
rename_str1 = [rename_expr[directionality[samples_table.loc[sample1, "kallisto_directionality"]]][0] for sample1 in list(samples_table.index.values)][0],
in_file_str2 = lambda wildcards, input: [os.path.basename(inp) for inp in input.str2],
rename_str2 = [rename_expr[directionality[samples_table.loc[sample1, "kallisto_directionality"]]][1] for sample1 in list(samples_table.index.values)][0],
genome_index = [os.path.abspath(os.path.join(
config["alfa_indexes"],
samples_table.loc[sample1, "organism"],
str(samples_table.loc[sample1, "index_size"]),
"ALFA", "sorted_genes")) for sample1 in list(samples_table.index.values)][0],
orientation = [directionality[samples_table.loc[sample1, "kallisto_directionality"]] for sample1 in list(samples_table.index.values)][0],
bg_and_sample_name = [sample1 + "_Signal.UniqueMultiple." +
rename_expr[directionality[samples_table.loc[sample1, "kallisto_directionality"]]][0] + ".bg " +
sample1 + "_Signal.UniqueMultiple." + rename_expr[directionality[samples_table.loc[sample1, "kallisto_directionality"]]][1] + ".bg " + sample1
for sample1 in list(samples_table.index.values)]
# singularity:
# "docker://zavolab/alfa:1.1.1"
conda: os.path.abspath("../../envs/env_alfa.yaml")
log: os.path.abspath(os.path.join(config["local_log"], "ALFA", "alfa_bg_all_samples.log"))
shell:
"""
mkdir -p {params.out_dir}; \
cd {params.out_dir}; \
cp {params.str1} . ; \
cp {params.str2} . ; \
rename 's/str1.out/{params.rename_str1}/' *str1.out.bg; \
rename 's/str2.out/{params.rename_str2}/' *str2.out.bg; \
(alfa -g {params.genome_index} \
--bedgraph {params.bg_and_sample_name} \
-s {params.orientation}) &> {log}; \
rm *{params.rename_str1}.bg *{params.rename_str2}.bg
"""
\ No newline at end of file
snakemake/paired_end.snakefile.smk
+ 12
− 13
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......@@ -354,25 +354,25 @@ rule star_rpm_paired_end:
"paired_end",
"{sample}",
"ALFA",
"STAR_Signal.Unique.str1.out.bg"),
"{sample}_Signal.Unique.str1.out.bg"),
os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"ALFA",
"STAR_Signal.UniqueMultiple.str1.out.bg")),
"{sample}_Signal.UniqueMultiple.str1.out.bg")),
str2 = (os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"ALFA",
"STAR_Signal.Unique.str2.out.bg"),
"{sample}_Signal.Unique.str2.out.bg"),
os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"ALFA",
"STAR_Signal.UniqueMultiple.str2.out.bg"))
"{sample}_Signal.UniqueMultiple.str2.out.bg"))
params:
out_dir = directory(os.path.join(config["output_dir"],
"paired_end",
......@@ -381,7 +381,7 @@ rule star_rpm_paired_end:
prefix = os.path.join(config["output_dir"],
"paired_end",
"{sample}",
"ALFA", "STAR_"),
"ALFA", "{sample}_"),
stranded = "Stranded"
singularity:
"docker://zavolab/star:2.6.0a"
......@@ -409,13 +409,13 @@ rule alfa_bg_paired_end:
"paired_end",
"{sample}",
"ALFA",
"STAR_Signal.UniqueMultiple.str1.out.bg"),
"{sample}_Signal.UniqueMultiple.str1.out.bg"),
str2 = os.path.join(
config["output_dir"],
"paired_end",
"{sample}",
"ALFA",
"STAR_Signal.UniqueMultiple.str2.out.bg"),
"{sample}_Signal.UniqueMultiple.str2.out.bg"),
gtf = lambda wildcards: os.path.join(config["alfa_indexes"], samples_table.loc[wildcards.sample, "organism"],
str(samples_table.loc[wildcards.sample, "index_size"]), "ALFA", "sorted_genes.stranded.ALFA_index")
output:
......@@ -438,12 +438,11 @@ rule alfa_bg_paired_end:
"{sample}",
"ALFA")),
orientation = lambda wildcards: directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]],
in_file_str1 = "STAR_Signal.UniqueMultiple.str1.out.bg",
rename_str1 = lambda wildcards: rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][0],
in_file_str2 = "STAR_Signal.UniqueMultiple.str2.out.bg",
rename_str2 = lambda wildcards: rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][1],
genome_index = lambda wildcards: os.path.abspath(os.path.join(config["alfa_indexes"], samples_table.loc[wildcards.sample, "organism"],
str(samples_table.loc[wildcards.sample, "index_size"]), "ALFA", "sorted_genes")),
in_file_str1 = lambda wildcards, input: os.path.basename(input.str1),
rename_str1 = lambda wildcards: wildcards.sample + "_" + rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][0],
in_file_str2 = lambda wildcards, input: os.path.basename(input.str2),
rename_str2 = lambda wildcards: wildcards.sample + "_" + rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][1],
genome_index = lambda wildcards, input: os.path.abspath(os.path.join(os.path.dirname(input.gtf), "sorted_genes")),
name = "{sample}"
singularity:
"docker://zavolab/alfa:1.1.1"
......
snakemake/single_end.snakefile.smk
+ 12
− 13
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......@@ -280,25 +280,25 @@ rule star_rpm_single_end:
"single_end",
"{sample}",
"ALFA",
"STAR_Signal.Unique.str1.out.bg"),
"{sample}_Signal.Unique.str1.out.bg"),
os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"ALFA",
"STAR_Signal.UniqueMultiple.str1.out.bg")),
"{sample}_Signal.UniqueMultiple.str1.out.bg")),
str2 = (os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"ALFA",
"STAR_Signal.Unique.str2.out.bg"),
"{sample}_Signal.Unique.str2.out.bg"),
os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"ALFA",
"STAR_Signal.UniqueMultiple.str2.out.bg"))
"{sample}_Signal.UniqueMultiple.str2.out.bg"))
params:
out_dir = directory(os.path.join(config["output_dir"],
"single_end",
......@@ -307,7 +307,7 @@ rule star_rpm_single_end:
prefix = os.path.join(config["output_dir"],
"single_end",
"{sample}",
"ALFA", "STAR_"),
"ALFA", "{sample}_"),
stranded = "Stranded"
singularity:
"docker://zavolab/star:2.6.0a"
......@@ -336,13 +336,13 @@ rule alfa_bg_single_end:
"single_end",
"{sample}",
"ALFA",
"STAR_Signal.UniqueMultiple.str1.out.bg"),
"{sample}_Signal.UniqueMultiple.str1.out.bg"),
str2 = os.path.join(
config["output_dir"],
"single_end",
"{sample}",
"ALFA",
"STAR_Signal.UniqueMultiple.str2.out.bg"),
"{sample}_Signal.UniqueMultiple.str2.out.bg"),
gtf = lambda wildcards: os.path.join(config["alfa_indexes"], samples_table.loc[wildcards.sample, "organism"],
str(samples_table.loc[wildcards.sample, "index_size"]), "ALFA", "sorted_genes.stranded.ALFA_index")
output:
......@@ -365,12 +365,11 @@ rule alfa_bg_single_end:
"{sample}",
"ALFA")),
orientation = lambda wildcards: directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]],
in_file_str1 = "STAR_Signal.UniqueMultiple.str1.out.bg",
rename_str1 = lambda wildcards: rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][0],
in_file_str2 = "STAR_Signal.UniqueMultiple.str2.out.bg",
rename_str2 = lambda wildcards: rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][1],
genome_index = lambda wildcards: os.path.abspath(os.path.join(config["alfa_indexes"], samples_table.loc[wildcards.sample, "organism"],
str(samples_table.loc[wildcards.sample, "index_size"]), "ALFA", "sorted_genes")),
in_file_str1 = lambda wildcards, input: os.path.basename(input.str1),
rename_str1 = lambda wildcards: wildcards.sample + "_" + rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][0],
in_file_str2 = lambda wildcards, input: os.path.basename(input.str2),
rename_str2 = lambda wildcards: wildcards.sample + "_" + rename_files[directionality[samples_table.loc[wildcards.sample, "kallisto_directionality"]]][1],
genome_index = lambda wildcards, input: os.path.abspath(os.path.join(os.path.dirname(input.gtf), "sorted_genes")),
name = "{sample}"
singularity:
"docker://zavolab/alfa:1.1.1"
......
tests/test_integration_workflow/test.local.sh
+ 2
− 1
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......@@ -20,7 +20,8 @@ snakemake \
--printshellcmds \
--rerun-incomplete \
--use-singularity \
--singularity-args="--bind ${PWD}"
--singularity-args="--bind ${PWD}" \
--use-conda
find results/ -type f -name \*\.gz -exec gunzip '{}' \;
find results/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \;
md5sum --check "expected_output.md5"
......
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