From 663d919427bb13e0e256218322fc078dc5ac30e2 Mon Sep 17 00:00:00 2001
From: Sukanya Denni <sukanya.denni@inrae.fr>
Date: Wed, 23 Nov 2022 13:59:33 +0100
Subject: [PATCH 1/2] added runtime log
---
workflow/Snakefile | 20 ++++++++-----
workflow/rules/00_runtime.smk | 54 +++++++++++++++++++++++++++++++++++
2 files changed, 67 insertions(+), 7 deletions(-)
create mode 100644 workflow/rules/00_runtime.smk
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 10ff558..036b09a 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -26,6 +26,9 @@ include: "rules/06_sym_link_hap.smk"
## AUTOMATIC REPORT
include: "rules/07_report.smk"
+## runtime
+include: "rules/00_runtime.smk"
+
###### get filenames for workflow ######
IDS=config["IDS"]
bamIDS=check_bam(config["root"] + "/" + config["resdir"] + "/" + config["bamdir"], IDS)
@@ -45,8 +48,6 @@ longqc_output = expand(res_path + "/{Bid}/{run}/01_raw_data_QC/02_longQC", zip,
fastqc_output = expand(res_path + "/{Fid}/{run}/01_raw_data_QC/01_fastQC/{Fid}_fastqc.{ext}", zip,
run=FID_RUN, Fid=fastqIDS, ext=["html", "zip"])
-
-
### REPORT
REP_ID = for_report(IDS)
RUNID_REG = run_id(REP_ID)
@@ -64,9 +65,6 @@ BUSCO_LIN_TRIO = busco_lin(REP_TRIO_ID)
report_trio_output = expand(res_path + "/{runid}/report_trio_{id}.{lin}.html", zip,
runid=RUNID_TRIO, id=REP_TRIO_ID, lin = BUSCO_LIN_TRIO)
-
-
-
### SYM LINK
## symbolic link to final assembly
symb_link1 = expand(res_path + "/{runid}/{id}_hap{n}.fa", zip,
@@ -80,7 +78,7 @@ cut_eval1 = expand(res_path + "/{runid}/02_genome_assembly/02_after_purge_dups_a
cut_eval2 = expand(res_path + "/{runid}/02_genome_assembly/02_after_purge_dups_assembly/00_assembly/{id}_hap{n}/cutoffs_graph_hap{n}.png", zip,
runid=RUNID_TRIO, id=REP_TRIO_ID, n=["1", "2"])
-# BUSCO
+## BUSCO
busco_reg = expand(res_path + "/{runid}/02_genome_assembly/01_raw_assembly/01_assembly_QC/busco/{id}_hap{n}/short_summary.specific.{lin}.{id}_hap{n}.txt", zip,
runid=RUNID_REG, id=REP_ID, n=["1", "2"], lin = BUSCO_LIN)
busco_purged_reg = expand(res_path + "/{runid}/02_genome_assembly/02_after_purge_dups_assembly/01_assembly_QC/busco/{id}_purged_hap{n}/short_summary.specific.{lin}.{id}_purged_hap{n}.txt", zip,
@@ -91,6 +89,12 @@ busco_trio = expand(res_path + "/{runid}/02_genome_assembly/01_raw_assembly/01_a
busco_purged_trio = expand(res_path + "/{runid}/02_genome_assembly/02_after_purge_dups_assembly/01_assembly_QC/busco/{id}_purged_hap{n}/short_summary.specific.{lin}.{id}_purged_hap{n}.txt", zip,
runid=RUNID_TRIO, id=REP_TRIO_ID, n=["1", "2"], lin = BUSCO_LIN_TRIO)
+## RUNTIME
+time = expand(res_path + "/{runid}/runtime.{id}.{lin}.txt", zip,
+ runid = RUNID_REG, id=REP_ID, lin=BUSCO_LIN)
+time_trio = expand(res_path + "/{runid}/runtime_trio.{id}.{lin}.txt", zip,
+ runid = RUNID_TRIO, id=REP_TRIO_ID, lin=BUSCO_LIN_TRIO)
+
rule_all_input_list = [
longqc_output,
fastqc_output,
@@ -103,7 +107,9 @@ rule_all_input_list = [
busco_reg,
busco_purged_reg,
busco_trio,
- busco_purged_trio
+ busco_purged_trio,
+ time,
+ time_trio
]
#### target files
diff --git a/workflow/rules/00_runtime.smk b/workflow/rules/00_runtime.smk
new file mode 100644
index 0000000..f53da68
--- /dev/null
+++ b/workflow/rules/00_runtime.smk
@@ -0,0 +1,54 @@
+rule start_time:
+ output:
+ temp(res_path + "/{runid}/runtime.txt")
+ priority: 20
+ run:
+ import time
+ start = time.time()
+ with open(output[0], "w") as out:
+ out.write(str(start))
+
+rule elasped_time:
+ input:
+ rules.start_time.output,
+ rules.rename_report.output
+ output:
+ res_path + "/{runid}/runtime.{id}.{lin}.txt"
+ run:
+ import time
+ from datetime import timedelta
+
+ with open(input[0], "r") as inp:
+ start = inp.read()
+
+ end = time.time()
+ elapsed_time = end - float(start)
+ td = timedelta(seconds=elapsed_time)
+
+ with open(output[0], "w") as out:
+ out.write("Runtime (hh:mm:ss): " + str(td))
+
+ # os.remove(input[0])
+
+
+rule elasped_time_trio:
+ input:
+ rules.start_time.output,
+ rules.rename_report_trio.output
+ output:
+ res_path + "/{runid}/runtime_trio.{id}.{lin}.txt"
+ run:
+ import time
+ from datetime import timedelta
+
+ with open(input[0], "r") as inp:
+ start = inp.read()
+
+ end = time.time()
+ elapsed_time = end - float(start)
+ td = timedelta(seconds=elapsed_time)
+
+ with open(output[0], "w") as out:
+ out.write("Runtime (hh:mm:ss): " + str(td))
+
+ # os.remove(input[0])
\ No newline at end of file
--
GitLab
From 6ab65b8d0a39f7632f9121914219000fd0b35c57 Mon Sep 17 00:00:00 2001
From: Sukanya Denni <sukanya.denni@inrae.fr>
Date: Thu, 24 Nov 2022 09:02:30 +0100
Subject: [PATCH 2/2] updated config with template
---
.config/masterconfig.yaml | 48 ++++++++-------------------------------
1 file changed, 9 insertions(+), 39 deletions(-)
diff --git a/.config/masterconfig.yaml b/.config/masterconfig.yaml
index 324bec9..60969e5 100644
--- a/.config/masterconfig.yaml
+++ b/.config/masterconfig.yaml
@@ -1,44 +1,6 @@
# absolute path to your desired output path
root: /gpfs/scratch/sdenni/wf/GenomAsm4pg
-### TEMPLATE
-IDS: ["E742-Rouge_de_Roussillon_ccs-20", "E742-CH-240_1-20"]
-
-# IDS_1:
- # path: path
- # bam: true
-# run: name
-# ploidy: 2
-# busco_lineage: eudi
-# mode: default
-
-# IDS_2:
- # path: path
- # bam: false
-# run: name
-# ploidy: 2
-# busco_lineage: eudi
-# mode: trio
-# p1: path
-# p2: path
-
-### TRIAL
-E742-Rouge_de_Roussillon_ccs-20:
- bam: False
- run: test_runid
- ploidy: 2
- busco_lineage: eudicots_odb10
- mode: default
-
-E742-CH-240_1-20:
- bam: False
- run: test_trio
- ploidy: 2
- busco_lineage: eudicots_odb10
- mode: trio
- p1: /scratch/sdenni/wf/GenomAsm4pg/workflow_results/00_raw_data/fastx_files/E742-CH-240_1.fasta.gz
- p2: /scratch/sdenni/wf/GenomAsm4pg/workflow_results/00_raw_data/fastx_files/E742-CH-240_1-20.fasta.gz
-
####################### prejob - data preparation #######################
# path to tar data
data: /path
@@ -48,8 +10,16 @@ get_all_tar_filename: True
tarIDS: "tar_filename"
####################### job - workflow #######################
-# list of fasta.gz names
+#### FILES YOU WANT TO RUN THE WORKFLOW ON
+IDS: ["sample_1"]
+### PARAMETERS
+## default assembly mode
+sample_1:
+ run: name
+ ploidy: 2
+ busco_lineage: eudicots_odb10
+ mode: default
####################### workflow output directories #######################
# results directory
--
GitLab