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Commit 27660897 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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gestion of gz

parent 23a2c768
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...@@ -181,7 +181,7 @@ if config["bowtie2_mapping"]["do"]: ...@@ -181,7 +181,7 @@ if config["bowtie2_mapping"]["do"]:
# indexing for bowtie2 # indexing for bowtie2
bowtie2_index_fasta = unpack(mapping_index) bowtie2_index_fasta = unpack(mapping_index)
bowtie2_index_log = "02-Mapping/bowtie2/logs/bowtie2_{REF}_indexing.log" bowtie2_index_log = "02-Mapping/{REF}/bowtie2/logs/bowtie2_{REF}_indexing.log"
bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}.1.bt2") bowtie2_index_output_done = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}.1.bt2")
bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}") bowtie2_index_output_prefix = os.path.join(config["genome"]["genome_directory"]+"{REF}/bowtie2/{REF}")
...@@ -211,7 +211,7 @@ if config["star_mapping"]["do"]: ...@@ -211,7 +211,7 @@ if config["star_mapping"]["do"]:
mapper += ["STAR"] mapper += ["STAR"]
star_index_fasta = unpack(mapping_index) star_index_fasta = unpack(mapping_index)
star_mapping_splice_file = unpack(annot_index) star_mapping_splice_file = unpack(annot_index)
star_index_log = "02-Mapping/STAR/logs/STAR_{REF}_indexing.log" star_index_log = "02-Mapping/{REF}/STAR/logs/STAR_{REF}_indexing.log"
star_index_output_done = config["genome"]["genome_directory"]+"/{REF}/STAR/SAindex" star_index_output_done = config["genome"]["genome_directory"]+"/{REF}/STAR/SAindex"
star_index_output_dir = config["genome"]["genome_directory"]+"/{REF}/STAR/" star_index_output_dir = config["genome"]["genome_directory"]+"/{REF}/STAR/"
...@@ -222,7 +222,7 @@ if config["star_mapping"]["do"]: ...@@ -222,7 +222,7 @@ if config["star_mapping"]["do"]:
star_mapping_pass1_input = adapters_output star_mapping_pass1_input = adapters_output
star_mapping_pass1_done = star_index_output_done star_mapping_pass1_done = star_index_output_done
star_mapping_pass1_index = star_index_output_dir star_mapping_pass1_index = star_index_output_dir
star_mapping_pass1_logs = "02-Mapping/STAR/logs/{SAMPLE}_{REF}_init.out" star_mapping_pass1_logs = "02-Mapping/{REF}/STAR//logs/{SAMPLE}_{REF}_init.out"
star_mapping_pass1_output_prefix = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_" star_mapping_pass1_output_prefix = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_"
star_mapping_pass1_junctions = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_SJ.out.tab" star_mapping_pass1_junctions = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_SJ.out.tab"
star_mapping_pass1_bam = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_Aligned.sortedByCoord.out.bam" star_mapping_pass1_bam = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_init_Aligned.sortedByCoord.out.bam"
...@@ -234,7 +234,7 @@ if config["star_mapping"]["do"]: ...@@ -234,7 +234,7 @@ if config["star_mapping"]["do"]:
star_mapping_pass2_input = adapters_output star_mapping_pass2_input = adapters_output
star_mapping_pass2_done = star_index_output_done star_mapping_pass2_done = star_index_output_done
star_mapping_pass2_index = star_index_output_dir star_mapping_pass2_index = star_index_output_dir
star_mapping_pass2_logs = "02-Mapping/STAR/logs/{SAMPLE}_{REF}.out" star_mapping_pass2_logs = "02-Mapping/{REF}/STAR//logs/{SAMPLE}_{REF}.out"
star_mapping_pass2_output_prefix = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_" star_mapping_pass2_output_prefix = "02-Mapping/{REF}/STAR/{SAMPLE}_{REF}_"
star_mapping_pass2_junctions = expand("02-Mapping/{{REF}}/STAR/{SAMPLE}_{{REF}}_init_SJ.out.tab", SAMPLE=samples) star_mapping_pass2_junctions = expand("02-Mapping/{{REF}}/STAR/{SAMPLE}_{{REF}}_init_SJ.out.tab", SAMPLE=samples)
star_mapping_pass2_bam = star_mapping_pass1_bam star_mapping_pass2_bam = star_mapping_pass1_bam
......
...@@ -28,14 +28,14 @@ rule alienTrimmer: ...@@ -28,14 +28,14 @@ rule alienTrimmer:
input: input:
fastq = adapters_input_fastq fastq = adapters_input_fastq
output: output:
adapters_output temp(adapters_output)
params: params:
wkdir = adapters_wkdir, wkdir = adapters_wkdir,
options = adapters_options, options = adapters_options,
adapters = config['adapters']['alien_file'], adapters = config['adapters']['alien_file'],
mode = adapters_mode, mode = adapters_mode,
min = adapters_min, min = adapters_min,
qual = adapters_qual qual = adapters_qual
singularity: singularity:
"rnaflow.img" "rnaflow.img"
shadow: "shallow" shadow: "shallow"
...@@ -48,11 +48,11 @@ rule alienTrimmer: ...@@ -48,11 +48,11 @@ rule alienTrimmer:
""" """
set +o pipefail set +o pipefail
tmp="{input}" tmp="{input}"
infiles=($tmp) infiles=($tmp)
tmp="{output}" tmp="{output}"
outfiles=($tmp) outfiles=($tmp)
# add options and adapter sequences # add options and adapter sequences
cmd+="AlienTrimmer -a {params.adapters} -l {params.min} -q {params.qual} {params.options}" cmd+="AlienTrimmer -a {params.adapters} -l {params.min} -q {params.qual} {params.options}"
......
...@@ -28,21 +28,20 @@ rule sortmerna: ...@@ -28,21 +28,20 @@ rule sortmerna:
fastq = sortmerna_input, fastq = sortmerna_input,
fasta = sortmerna_fasta fasta = sortmerna_fasta
output: output:
rRNA = sortmerna_outfile_rRNA, rRNA = temp(sortmerna_outfile_rRNA),
no_rRNA = sortmerna_outfile_no_rRNA no_rRNA = temp(sortmerna_outfile_no_rRNA)
singularity: singularity:
"rnaflow.img" "rnaflow.img"
log: log:
err = sortmerna_logs_err, err = sortmerna_logs_err,
out = sortmerna_logs_out out = sortmerna_logs_out
shadow: "shallow"
threads: 6 threads: 6
envmodules: envmodules:
"sortmerna/2.1b" "sortmerna/2.1b"
shell: shell:
""" """
set +o pipefail set +o pipefail
#tmp="{input.fastq}" #tmp="{input.fastq}"
#infiles=($tmp) #infiles=($tmp)
fasta="{input.fasta}" fasta="{input.fasta}"
index=${{fasta%.fa}} index=${{fasta%.fa}}
...@@ -53,11 +52,7 @@ rule sortmerna: ...@@ -53,11 +52,7 @@ rule sortmerna:
fi fi
sortmerna --ref ${{fasta}},${{index}} -a {threads} --reads {input.fastq} --aligned outfile_rRNA --fastx --sam --num_alignments 1 --other outfile_noRNA --log -v > {log.out} 2> {log.err} sortmerna --ref ${{fasta}},${{index}} -a {threads} --reads {input.fastq} --aligned {output.rRNA} --fastx --sam --num_alignments 1 --other {output.no_rRNA} --log -v > {log.out} 2> {log.err}
pigz -fc outfile_rRNA > {output.rRNA}
pigz -fc outfile_noRNA {output.no_rRNA}
""" """
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