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merged devel into master_new
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@sklarz-bgu
sklarz-bgu committed Jun 10, 2019
2 parents b69efc2 + 05cb274 commit 0bf6d61
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Showing 67 changed files with 7,235 additions and 1,793 deletions.
1 change: 1 addition & 0 deletions .gitignore
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@@ -1,4 +1,5 @@
*.bck
*.bak
*.pyc
git-gui*
not_for_publication
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2 changes: 1 addition & 1 deletion MANIFEST.in
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@@ -1 +1 @@
recursive-include neatseq_flow_modules *.R *.fasta *.tsv *.yml
recursive-include neatseq_flow_modules *.R *.fasta *.tsv *.yml *.pl
71 changes: 63 additions & 8 deletions Workflows/BLAST_db.yaml
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Expand Up @@ -49,7 +49,7 @@ Step_params:
-dbtype: nucl
############################ 2. BLAST external fasta against genomic sequences
blst_asmbl:
module: blast
module: blast_old
base: mkblst_nucl
script_path: '{Vars.paths.blast}/tblastn'
qsub_params:
Expand All @@ -68,7 +68,7 @@ Step_params:
module: parse_blast
base: blst_asmbl
script_path: {Vars.paths.parse_blast}
blast_merge_path: {Vars.paths.compare_blast_parsed_reports}
# blast_merge_path: {Vars.paths.compare_blast_parsed_reports}
scope: sample
redirects:
--dbtable: {Vars.databases.gene_list.table}
Expand All @@ -94,7 +94,7 @@ Step_params:
--strain:
############################ 6. BLAST predicted genes against swissprot
blst_genes:
module: blast
module: blast_old
base: prokka_asmbl
script_path: '{Vars.paths.blast}/blastx'
qsub_params:
Expand All @@ -112,8 +112,11 @@ Step_params:
parse_blst_genes:
module: parse_blast
base: blst_genes
script_path: {Vars.paths.parse_blast}
blast_merge_path: {Vars.paths.compare_blast_parsed_reports}
# script_path: {Vars.paths.parse_blast}
script_path: Rscript /path/to/parse_blast.R
blast_merge:
path: #{Vars.paths.compare_blast_parsed_reports}
redirects: --variable evalue --full_txt_output --name qseqid
scope: sample
redirects:
--dbtable: {Vars.databases.uniprot_sprot.table}
Expand All @@ -123,7 +126,7 @@ Step_params:
bitscore score pident qframe"'
############################ 7. BLAST predicted genes against swissprot - Alternative module
blst_genes_alt:
module: blast_new
module: blast
base: prokka_asmbl
script_path: '{Vars.paths.blast}/blastx'
redirects:
Expand All @@ -133,7 +136,7 @@ Step_params:
querytype: nucl # Use the 'nucl' output from prokka
############################ BONUS. BLAST predicted genes against assembly
blst_genes_asmbl:
module: blast_new
module: blast
base: [prokka_asmbl,mkblst_nucl]
script_path: '{Vars.paths.blast}/blastn'
redirects:
Expand All @@ -147,11 +150,63 @@ Step_params:
module: parse_blast
base: blst_genes_asmbl
script_path: {Vars.paths.parse_blast}
blast_merge_path: {Vars.paths.compare_blast_parsed_reports}
blast_merge:
path: {Vars.paths.compare_blast_parsed_reports}
redirects:
--variable: evalue
--full_txt_output:
--name: qseqid

scope: sample
redirects:
--dbtable: {Vars.databases.gene_list.table}
--max_evalue: 1e-7
--min_bitscore: 100
--names: '"qseqid sallseqid qlen slen qstart qend sstart send length evalue
bitscore score pident qframe"'

############# Trying project scope blast and parse
merge_fasta:
module: merge_table
base: merge_nucl
script_path:
scope: project
type: fasta.nucl
header: 0

mkblst_nucl_project:
module: makeblastdb
base: merge_fasta
script_path: {Vars.paths.makeblastdb}
scope: project
qsub_params:
-pe: shared 20
redirects:
-dbtype: nucl

blst_genes_project:
module: blast
base: mkblst_nucl_project
script_path: '{Vars.paths.blast}/blastn'
redirects:
-evalue: 0.0001
db: project
query: project
querytype: nucl # Use the 'nucl' output from prokka
dbtype: nucl # Use the 'nucl' output from prokka

parse_tbl_blst_project:
module: parse_blast
base: blst_genes_project
script_path: {Vars.paths.parse_blast}
scope: project
extract_fasta:
redirects:
--dbtable: {Vars.databases.gene_list.table}
--max_evalue: 1e-7
--min_bitscore: 100
--names: '"qseqid sallseqid qlen slen qstart qend sstart send length evalue
bitscore score pident qframe"'



22 changes: 16 additions & 6 deletions Workflows/BLAST_fasta.yaml
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Expand Up @@ -102,7 +102,7 @@ Step_params:
-dbtype: nucl
############################ 4. BLAST external fasta against assembly
blst_asmbl:
module: blast
module: blast_old
base: mkblst_asmbl
script_path: '{Vars.paths.blast}/tblastn'
qsub_params:
Expand All @@ -129,7 +129,12 @@ Step_params:
module: parse_blast
base: blst_asmbl
script_path: {Vars.paths.parse_blast}
blast_merge_path: {Vars.paths.compare_blast_parsed_reports}
blast_merge:
path: {Vars.paths.compare_blast_parsed_reports}
redirects:
--variable: evalue
--full_txt_output:
--name: qseqid
scope: sample
redirects:
--dbtable: {Vars.databases.VFDB.table}
Expand All @@ -155,7 +160,7 @@ Step_params:
--strain:
############################ 6. BLAST predicted genes against swissprot
blst_genes:
module: blast
module: blast_old
base: prokka_asmbl
script_path: '{Vars.paths.blast}/blastx'
qsub_params:
Expand All @@ -174,17 +179,22 @@ Step_params:
module: parse_blast
base: blst_genes
script_path: {Vars.paths.parse_blast}
blast_merge_path: {Vars.paths.compare_blast_parsed_reports}
scope: sample
redirects:
--dbtable: {Vars.databases.uniprot_sprot.table}
--max_evalue: 1e-7
--min_bitscore: 100
--names: '"qseqid sallseqid qlen slen qstart qend sstart send length evalue
bitscore score pident qframe"'
blast_merge:
path: {Vars.paths.compare_blast_parsed_reports}
redirects:
--variable: evalue
--full_txt_output:
--name: qseqid
############################ 7. BLAST predicted genes against swissprot - Alternative module
blst_genes_alt:
module: blast_new
module: blast
base: prokka_asmbl
script_path: '{Vars.paths.blast}/blastx'
db: {Vars.databases.uniprot_sprot.blastdb}
Expand All @@ -194,7 +204,7 @@ Step_params:
-evalue: 0.0001
############################ BONUS. BLAST predicted genes against assembly
blst_genes_asmbl:
module: blast_new
module: blast
base: [prokka_asmbl,mkblst_asmbl]
script_path: '{Vars.paths.blast}/blastn'
db: sample
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18 changes: 9 additions & 9 deletions Workflows/BLAST_test.yaml
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Expand Up @@ -18,7 +18,7 @@ Description: |
4. Searching the assembly using a fasta query file.
5. Annotation of the assemblies using prokka
6. Using the resulting predicted gene sequences to search a BLAST database.
7. Using the alternative BLAST module ('blast_new') to search the assembly for the predicted genes.
7. Using the BLAST module ('blast') to search the assembly for the predicted genes.
Note. Module 'parse_blast' uses a program for parsing tabular BLAST tables. The code is freelly accessible at https://github.com/bioinfo-core-BGU/parse_blast
Expand Down Expand Up @@ -84,7 +84,7 @@ Step_params:


Blast_1a:
module: blast_new
module: blast
base: [Mkblst_prj, Mkblst_smp]
script_path: '{Vars.paths.blast}/blastx'
db: sample
Expand All @@ -95,7 +95,7 @@ Step_params:
-evalue: 0.0001

Blast_1b:
module: blast_new
module: blast
base: [Mkblst_prj, Mkblst_smp]
script_path: '{Vars.paths.blast}/blastx'
db: sample
Expand All @@ -107,7 +107,7 @@ Step_params:
# stop_and_show_input:

Blast_1c:
module: blast_new
module: blast
base: [Mkblst_prj, Mkblst_smp]
script_path: '{Vars.paths.blast}/blastx'
db: project
Expand All @@ -118,7 +118,7 @@ Step_params:
-evalue: 0.0001

Blast_1d:
module: blast_new
module: blast
base: [Mkblst_prj, Mkblst_smp]
script_path: '{Vars.paths.blast}/blastx'
db: project
Expand All @@ -130,7 +130,7 @@ Step_params:


Blast_2a:
module: blast_new
module: blast
base: [Mkblst_prj, Mkblst_smp]
script_path: '{Vars.paths.blast}/blastx'
db: sample
Expand All @@ -141,7 +141,7 @@ Step_params:
-evalue: 0.0001

Blast_2b:
module: blast_new
module: blast
base: [Mkblst_prj, Mkblst_smp]
script_path: '{Vars.paths.blast}/blastx'
db: project
Expand All @@ -152,7 +152,7 @@ Step_params:
-evalue: 0.0001

Blast_3a:
module: blast_new
module: blast
base: [Mkblst_prj, Mkblst_smp]
script_path: '{Vars.paths.blast}/blastx'
db: /path/to/blastdb
Expand All @@ -163,7 +163,7 @@ Step_params:
-evalue: 0.0001

Blast_3b:
module: blast_new
module: blast
base: [Mkblst_prj, Mkblst_smp]
script_path: '{Vars.paths.blast}/blastx'
db: /path/to/blastdb
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7 changes: 5 additions & 2 deletions Workflows/Basic_Preparation.yaml
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@@ -1,4 +1,5 @@
Global_params:
# Executor: Local
Default_wait: 10
Qsub_opts: -V -cwd
Qsub_path: /path/to/qsub/bin
Expand Down Expand Up @@ -71,7 +72,6 @@ Step_params:
- ..guess..
intermediate:
tag: basic
# stop_and_show:

fastq_screen_alt1:
module: fastq_screen
Expand Down Expand Up @@ -103,6 +103,9 @@ Step_params:
--tag:
--force:
--threads: 10
# conda:
# path: JKJLJLJL
# env:

fqc_merge1:
module: fastqc_html
Expand Down Expand Up @@ -168,7 +171,7 @@ Step_params:
base: fqc_trimgal
script_path: {Vars.paths.multiqc}
tag:
SKIP: False
SKIP: #False
redirects:
--interactive:
# stop_and_show:
2 changes: 1 addition & 1 deletion Workflows/ChIP_seq.yaml
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Expand Up @@ -31,7 +31,7 @@ Global_params:
conda:
path:
env: ChIP_seq_WF
# module_path: ../neatseq_flow_modules
module_path: ../neatseq_flow_modules


Vars:
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