diff --git a/snakemodules/analysis.smk b/snakemodules/analysis.smk
index 7fef97407653e379804b3e73d221887b4ba03a31..a32b477895c11c97c1d368e9d9c09f9221b6b02f 100644
--- a/snakemodules/analysis.smk
+++ b/snakemodules/analysis.smk
@@ -44,6 +44,9 @@ if config["SICKLE"]=="no":
group: "unmapped_analysis"
notebook:
os.path.join(WORKFLOW_PATH,"snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb")
+
+
+
if config["remove_contamination"]=="yes":
@@ -91,6 +94,7 @@ if config["SICKLE"]=="no":
group: "unmapped_analysis_no_filtler_after_clean"
notebook:
os.path.join(WORKFLOW_PATH,"snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb")
+
elif config["SICKLE"]=="yes":
@@ -139,6 +143,8 @@ elif config["SICKLE"]=="yes":
group: "unmapped_analysis_before_filter"
notebook:
os.path.join(WORKFLOW_PATH,"snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb")
+
+
rule email_unmapped_analysis_after_filter:
@@ -185,6 +191,8 @@ elif config["SICKLE"]=="yes":
group: "unmapped_analysis_after_filter"
notebook:
os.path.join(WORKFLOW_PATH,"snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb")
+
+
elif config["remove_contamination"]=="yes":
@@ -232,6 +240,7 @@ elif config["SICKLE"]=="yes":
group: "unmapped_analysis_before_clean_filter"
notebook:
os.path.join(WORKFLOW_PATH,"snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb")
+
rule email_unmapped_analysis_after_clean:
@@ -324,6 +333,7 @@ elif config["SICKLE"]=="yes":
group: "unmapped_analysis_after_clean_filter"
notebook:
os.path.join(WORKFLOW_PATH,"snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb")
+
@@ -472,4 +482,3 @@ rule coverage_analysis:
group: "coverage_analysis"
notebook:
os.path.join(WORKFLOW_PATH,"snakemodules/notebooks/contig_coverage_heatmap.py.ipynb")
-
diff --git a/snakemodules/contigmap.smk b/snakemodules/contigmap.smk
index 84d8bfb35858b05c69132ecd280f956d9603fa7e..165d41af90fcf4dcb6c426a3c58256f8b42c083b 100644
--- a/snakemodules/contigmap.smk
+++ b/snakemodules/contigmap.smk
@@ -169,7 +169,7 @@ rule coordinate_sort_unsorted:
input:
WORK_DIR + "/{sample}/merged.bam"
output:
- WORK_DIR + "/{sample}/non_ref_new.bam"
+ temp(WORK_DIR + "/{sample}/non_ref_new.bam")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
@@ -192,7 +192,7 @@ rule index_sorted:
input:
WORK_DIR + "/{sample}/non_ref_new.bam"
output:
- WORK_DIR + "/{sample}/non_ref_new.bam.bai"
+ temp(WORK_DIR + "/{sample}/non_ref_new.bam.bai")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
diff --git a/snakemodules/crop_remapped.smk b/snakemodules/crop_remapped.smk
index d91fafc0e4ad8531cd16ed7df22c17f6cceaf0f0..87a3c96b52a13182fd06897f951ad9507d2fa859 100644
--- a/snakemodules/crop_remapped.smk
+++ b/snakemodules/crop_remapped.smk
@@ -23,9 +23,9 @@ if config["SICKLE"]=="no":
find_bam_file
# INPUT_DIR + "/{sample}/{sample}.bam"
output:
- WORK_DIR + "/{sample}/single.fastq",
- WORK_DIR + "/{sample}/paired.1.fastq",
- WORK_DIR + "/{sample}/paired.2.fastq",
+ temp(WORK_DIR + "/{sample}/single.fastq"),
+ temp(WORK_DIR + "/{sample}/paired.1.fastq"),
+ temp(WORK_DIR + "/{sample}/paired.2.fastq"),
temp(WORK_DIR + "/{sample}/mates.bam"),
WORK_DIR + "/{sample}/POPINS_SAMPLE_INFO"
params:
@@ -56,7 +56,7 @@ if config["SICKLE"]=="no":
os.path.join(RESULTS_DIR, "read_numbers.png") if config["ANALYSIS"]=="yes" else [],
mates = WORK_DIR + "/{sample}/mates.bam"
output:
- WORK_DIR + "/{sample}/non_ref.bam"
+ temp(WORK_DIR + "/{sample}/non_ref.bam")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
@@ -78,9 +78,9 @@ elif config["SICKLE"]=="yes":
input:
INPUT_DIR + "/{sample}/{sample}.bam"
output:
- WORK_DIR + "/{sample}/single.fastq",
- WORK_DIR + "/{sample}/paired.1.fastq",
- WORK_DIR + "/{sample}/paired.2.fastq",
+ temp(WORK_DIR + "/{sample}/single.fastq"),
+ temp(WORK_DIR + "/{sample}/paired.1.fastq"),
+ temp(WORK_DIR + "/{sample}/paired.2.fastq"),
temp(WORK_DIR + "/{sample}/mates.bam"),
WORK_DIR + "/{sample}/POPINS_SAMPLE_INFO"
params:
@@ -109,7 +109,7 @@ elif config["SICKLE"]=="yes":
# os.path.join(RESULTS_DIR, "read_numbers.png") if config["ANALYSIS"]=="yes" else [],
mates = WORK_DIR + "/{sample}/mates.bam"
output:
- WORK_DIR + "/{sample}/non_ref.bam"
+ temp(WORK_DIR + "/{sample}/non_ref.bam")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
diff --git a/snakemodules/crop_unmapped.smk b/snakemodules/crop_unmapped.smk
index 1f0e9a3fa40ec6751cf08400c4b744c3c1f0897c..dc98159931fa7fc2ea56c1f3e9dfb0ef46e136d0 100644
--- a/snakemodules/crop_unmapped.smk
+++ b/snakemodules/crop_unmapped.smk
@@ -21,9 +21,9 @@ if config["SICKLE"]=="no":
find_bam_file
# INPUT_DIR + "/{sample}/{sample}.bam"
output:
- WORK_DIR + "/{sample}/single.fastq",
- WORK_DIR + "/{sample}/paired.1.fastq",
- WORK_DIR + "/{sample}/paired.2.fastq",
+ temp(WORK_DIR + "/{sample}/single.fastq"),
+ temp(WORK_DIR + "/{sample}/paired.1.fastq"),
+ temp(WORK_DIR + "/{sample}/paired.2.fastq"),
temp(WORK_DIR + "/{sample}/mates.bam"),
WORK_DIR + "/{sample}/POPINS_SAMPLE_INFO"
params:
@@ -54,7 +54,7 @@ if config["SICKLE"]=="no":
os.path.join(RESULTS_DIR, "read_numbers.png") if config["ANALYSIS"]=="yes" else [],
mates = WORK_DIR + "/{sample}/mates.bam"
output:
- WORK_DIR + "/{sample}/non_ref.bam"
+ temp(WORK_DIR + "/{sample}/non_ref.bam")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
@@ -76,9 +76,9 @@ elif config["SICKLE"]=="yes":
input:
INPUT_DIR + "/{sample}/{sample}.bam"
output:
- WORK_DIR + "/{sample}/single.fastq",
- WORK_DIR + "/{sample}/paired.1.fastq",
- WORK_DIR + "/{sample}/paired.2.fastq",
+ temp(WORK_DIR + "/{sample}/single.fastq"),
+ temp(WORK_DIR + "/{sample}/paired.1.fastq"),
+ temp(WORK_DIR + "/{sample}/paired.2.fastq"),
temp(WORK_DIR + "/{sample}/mates.bam"),
WORK_DIR + "/{sample}/POPINS_SAMPLE_INFO"
params:
@@ -107,7 +107,7 @@ elif config["SICKLE"]=="yes":
# os.path.join(RESULTS_DIR, "read_numbers.png") if config["ANALYSIS"]=="yes" else [],
mates = WORK_DIR + "/{sample}/mates.bam"
output:
- WORK_DIR + "/{sample}/non_ref.bam"
+ temp(WORK_DIR + "/{sample}/non_ref.bam")
resources:
mem_per_thread = resources["samtools_multithread"]["mem_per_thread"],
mem_mb = lambda wildcards, input, threads, attempt: resources["samtools_multithread"]["mem_per_thread"] * threads,
diff --git a/snakemodules/genotype.smk b/snakemodules/genotype.smk
index b489683bf064fd230fe5cb3fa375c95b48a08378..f61bd44305bff4973c81b349ef43ddc9c2389a44 100644
--- a/snakemodules/genotype.smk
+++ b/snakemodules/genotype.smk
@@ -28,7 +28,7 @@ rule popins2_genotype:
input:
rules.sort_vcf.output
output:
- WORK_DIR + "/{sample}/insertions.vcf"
+ temp(WORK_DIR + "/{sample}/insertions.vcf")
resources:
mem_mb = resources["standard_2G"]["mem"],
runtime = resources["standard_2G"]["time"]
diff --git a/snakemodules/kraken.smk b/snakemodules/kraken.smk
index ea2abfed170aee5fc7ab3e09897d3bb1a0bf82c1..e53b0e461cd25cab2b01993a5c67415780828fc9 100644
--- a/snakemodules/kraken.smk
+++ b/snakemodules/kraken.smk
@@ -8,15 +8,15 @@ rule kraken_map:
p2 = WORK_DIR + "/{sample}/paired.2.fastq"
output:
single_report = WORK_DIR + "/{sample}/contaminate_info/single_report.txt",
- single_output = WORK_DIR + "/{sample}/contaminate_info/single_output.txt",
- u_single = WORK_DIR + "/{sample}/contaminate_info/useq_single.fq",
- c_single = WORK_DIR + "/{sample}/contaminate_info/cseq_single.fq",
+ single_output = temp(WORK_DIR + "/{sample}/contaminate_info/single_output.txt"),
+ u_single = temp(WORK_DIR + "/{sample}/contaminate_info/useq_single.fq"),
+ c_single = temp(WORK_DIR + "/{sample}/contaminate_info/cseq_single.fq"),
paired_report = WORK_DIR + "/{sample}/contaminate_info/paired_report.txt",
- paired_output = WORK_DIR + "/{sample}/contaminate_info/paired_output.txt",
- c_paired_1 = WORK_DIR + "/{sample}/contaminate_info/cseqs_1.fq",
- c_paired_2 = WORK_DIR + "/{sample}/contaminate_info/cseqs_2.fq",
- u_paired_1 = WORK_DIR + "/{sample}/contaminate_info/useqs_1.fq",
- u_paired_2 = WORK_DIR + "/{sample}/contaminate_info/useqs_2.fq"
+ paired_output = temp(WORK_DIR + "/{sample}/contaminate_info/paired_output.txt"),
+ c_paired_1 = temp(WORK_DIR + "/{sample}/contaminate_info/cseqs_1.fq"),
+ c_paired_2 = temp(WORK_DIR + "/{sample}/contaminate_info/cseqs_2.fq"),
+ u_paired_1 = temp(WORK_DIR + "/{sample}/contaminate_info/useqs_1.fq"),
+ u_paired_2 = temp(WORK_DIR + "/{sample}/contaminate_info/useqs_2.fq")
singularity:
"docker://staphb/kraken2:latest"
conda:
@@ -63,9 +63,9 @@ rule obtain_classified_human_reads:
paired_fq2 = rules.kraken_map.output.c_paired_2,
script= os.path.join(WORKFLOW_PATH,config["python_script"])
output:
- hc_single = WORK_DIR + "/{sample}/contaminate_info/human_classified_single.fastq",
- hc_paired_1 = WORK_DIR + "/{sample}/contaminate_info/human_classified_paired_1.fastq",
- hc_paired_2 = WORK_DIR + "/{sample}/contaminate_info/human_classified_paired_2.fastq"
+ hc_single = temp(WORK_DIR + "/{sample}/contaminate_info/human_classified_single.fastq"),
+ hc_paired_1 = temp(WORK_DIR + "/{sample}/contaminate_info/human_classified_paired_1.fastq"),
+ hc_paired_2 = temp(WORK_DIR + "/{sample}/contaminate_info/human_classified_paired_2.fastq")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/biopython.yml")
resources:
@@ -146,7 +146,7 @@ rule samtools_remap_classified_human:
sam = rules.bwa_remap_classified_human.output.remapped_sam
output:
remapped_unsorted = temp(WORK_DIR + "/{sample}/contaminate_info/remapped_human_unsorted.bam"),
- remapped_bam = WORK_DIR + "/{sample}/contaminate_info/remapped.bam"
+ remapped_bam = temp(WORK_DIR + "/{sample}/contaminate_info/remapped.bam")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
@@ -169,7 +169,7 @@ rule index_reads:
input:
bam = rules.samtools_remap_classified_human.output.remapped_bam
output:
- bai = WORK_DIR + "/{sample}/contaminate_info/remapped.bam.bai"
+ bai = temp(WORK_DIR + "/{sample}/contaminate_info/remapped.bam.bai")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
@@ -191,9 +191,9 @@ rule crop_remapped:
bam = rules.samtools_remap_classified_human.output.remapped_bam,
bai = rules.index_reads.output.bai
output:
- single = WORK_DIR + "/{sample}/remapped_single.fastq",
- p1 = WORK_DIR + "/{sample}/remapped_paired.1.fastq",
- p2 = WORK_DIR + "/{sample}/remapped_paired.2.fastq",
+ single = temp(WORK_DIR + "/{sample}/remapped_single.fastq"),
+ p1 = temp(WORK_DIR + "/{sample}/remapped_paired.1.fastq"),
+ p2 = temp(WORK_DIR + "/{sample}/remapped_paired.2.fastq"),
unsorted = temp(WORK_DIR + "/{sample}/remapped_mates.unsorted.bam")
resources:
mem_mb = resources["standard_2G"]["mem"],
@@ -220,7 +220,7 @@ rule remapping_samsort_mates:
input:
WORK_DIR + "/{sample}/remapped_mates.unsorted.bam"
output:
- WORK_DIR + "/{sample}/remapped_mates.bam"
+ temp(WORK_DIR + "/{sample}/remapped_mates.bam")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/samtools.yml")
resources:
@@ -242,7 +242,7 @@ rule merge_set_mate:
non_ref = WORK_DIR + "/{sample}/non_ref.bam",
rm_ref = WORK_DIR + "/{sample}/remapped_mates.bam"
output:
- WORK_DIR + "/{sample}/remapped_non_ref.bam"
+ temp(WORK_DIR + "/{sample}/remapped_non_ref.bam")
resources:
mem_mb = resources["standard_2G"]["mem"],
runtime = resources["standard_2G"]["time"]
@@ -270,9 +270,9 @@ rule contaminate_removed:
u_p1 = rules.kraken_map.output.u_paired_1,
u_p2 = rules.kraken_map.output.u_paired_2
output:
- single_clean = WORK_DIR + "/{sample}/single_clean.fastq",
- p1_clean = WORK_DIR + "/{sample}/paired_1_clean.fastq",
- p2_clean = WORK_DIR + "/{sample}/paired_2_clean.fastq"
+ single_clean = temp(WORK_DIR + "/{sample}/single_clean.fastq"),
+ p1_clean = temp(WORK_DIR + "/{sample}/paired_1_clean.fastq"),
+ p2_clean = temp(WORK_DIR + "/{sample}/paired_2_clean.fastq")
resources:
mem_mb = resources["standard_2G"]["mem"],
runtime = resources["standard_2G"]["time"]
diff --git a/snakemodules/minia.smk b/snakemodules/minia.smk
index a08164343074e06dda7beed00dca1ca9959eb7b7..b2d318b1193b923f89485ac3bc9181035d3eacd1 100644
--- a/snakemodules/minia.smk
+++ b/snakemodules/minia.smk
@@ -8,7 +8,7 @@ if config["SICKLE"]=="yes":
pair_1 = WORK_DIR + "/{sample}/sickle.paired_1_clean.fastq",
pair_2 = WORK_DIR + "/{sample}/sickle.paired_2_clean.fastq"
output:
- WORK_DIR + "/{sample}/{assemblr}.contigs.fa"
+ temp(WORK_DIR + "/{sample}/{assemblr}.contigs.fa")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/py27.yml")
resources:
@@ -36,7 +36,7 @@ if config["SICKLE"]=="yes":
pair_1 = WORK_DIR + "/{sample}/sickle.paired.1.fastq",
pair_2 = WORK_DIR + "/{sample}/sickle.paired.2.fastq"
output:
- WORK_DIR + "/{sample}/{assemblr}.contigs.fa"
+ temp(WORK_DIR + "/{sample}/{assemblr}.contigs.fa")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/py27.yml")
resources:
@@ -64,7 +64,7 @@ elif config["SICKLE"]=="no":
pair_1 = WORK_DIR + "/{sample}/paired_1_clean.fastq",
pair_2 = WORK_DIR + "/{sample}/paired_2_clean.fastq"
output:
- WORK_DIR + "/{sample}/{assemblr}.contigs.fa"
+ temp(WORK_DIR + "/{sample}/{assemblr}.contigs.fa")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/py27.yml")
resources:
@@ -92,7 +92,7 @@ elif config["SICKLE"]=="no":
pair_1 = WORK_DIR + "/{sample}/paired.1.fastq",
pair_2 = WORK_DIR + "/{sample}/paired.2.fastq"
output:
- WORK_DIR + "/{sample}/{assemblr}.contigs.fa"
+ temp(WORK_DIR + "/{sample}/{assemblr}.contigs.fa")
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/py27.yml")
resources:
diff --git a/snakemodules/position.smk b/snakemodules/position.smk
index d96a633305dd1dfbb04bc1ed5a4cebb2546f0ed6..d1769ce74f8825602c23455c8784fff10ce7f479 100644
--- a/snakemodules/position.smk
+++ b/snakemodules/position.smk
@@ -8,7 +8,7 @@ if config["remove_contamination"] == 'yes':
os.path.join(RESULTS_DIR, "heatmap_coverage.png") if config["ANALYSIS"]=="yes" else [],
WORK_DIR + "/{sample}/remapped_non_ref.bam"
output:
- WORK_DIR + "/{sample}/locations.txt"
+ temp(WORK_DIR + "/{sample}/locations.txt")
resources:
mem_mb = resources["standard_4G"]["mem"],
runtime = resources["standard_4G"]["time"]
@@ -34,7 +34,7 @@ elif config["remove_contamination"] == 'no':
os.path.join(RESULTS_DIR, "heatmap_coverage.png") if config["ANALYSIS"]=="yes" else [],
expand(WORK_DIR + "/{s}/{f}", s=SAMPLES, f=["non_ref_new.bam","non_ref.bam"])
output:
- WORK_DIR + "/{sample}/locations.txt"
+ temp(WORK_DIR + "/{sample}/locations.txt")
resources:
mem_mb = resources["standard_4G"]["mem"],
runtime = resources["standard_4G"]["time"]
diff --git a/snakemodules/velvet.smk b/snakemodules/velvet.smk
index 1f5ba1916f69de41b72d5ebdf90d9cddf747f6ab..7dcb2d45d01e5677dcc0fe8d0c38a7025882a283 100644
--- a/snakemodules/velvet.smk
+++ b/snakemodules/velvet.smk
@@ -7,7 +7,7 @@ if config["SICKLE"]=="yes":
pair_1 = WORK_DIR + "/{sample}/sickle.paired_1_clean.fastq",
pair_2 = WORK_DIR + "/{sample}/sickle.paired_2_clean.fastq"
output:
- WORK_DIR + "/{sample}/{assemblr}.contigs.fa"
+ temp(WORK_DIR + "/{sample}/{assemblr}.contigs.fa")
params:
kmerlength = config["kmerlength"]
conda:
@@ -37,7 +37,7 @@ if config["SICKLE"]=="yes":
pair_1 = WORK_DIR + "/{sample}/sickle.paired.1.fastq",
pair_2 = WORK_DIR + "/{sample}/sickle.paired.2.fastq"
output:
- WORK_DIR + "/{sample}/{assemblr}.contigs.fa"
+ temp(WORK_DIR + "/{sample}/{assemblr}.contigs.fa")
params:
kmerlength = config["kmerlength"]
conda:
@@ -67,7 +67,7 @@ elif config["SICKLE"]=="no":
pair_1 = WORK_DIR + "/{sample}/paired_1_clean.fastq",
pair_2 = WORK_DIR + "/{sample}/paired_2_clean.fastq"
output:
- WORK_DIR + "/{sample}/{assemblr}.contigs.fa"
+ temp(WORK_DIR + "/{sample}/{assemblr}.contigs.fa")
params:
kmerlength = config["kmerlength"]
conda:
@@ -97,7 +97,7 @@ elif config["SICKLE"]=="no":
pair_1 = WORK_DIR + "/{sample}/paired.1.fastq",
pair_2 = WORK_DIR + "/{sample}/paired.2.fastq"
output:
- WORK_DIR + "/{sample}/{assemblr}.contigs.fa"
+ temp(WORK_DIR + "/{sample}/{assemblr}.contigs.fa")
params:
kmerlength = config["kmerlength"]
conda: