From 15615e09f5c5109170d2f28fd6be289517031a31 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20FERNANDEZ=20NU=C3=91EZ?=
<fernandez.nunez.nicolas@gmail.com>
Date: Fri, 18 Nov 2022 14:12:48 +0100
Subject: [PATCH] Update v.2022.11
---
config/config.yaml | 12 ++--
config/fastq-screen_bowtie2.conf | 69 +++++++++++++++++++
...astq-screen.conf => fastq-screen_bwa.conf} | 2 +-
workflow/rules/indexing_genomes.smk | 2 +-
workflow/rules/quality_control.smk | 2 +-
5 files changed, 80 insertions(+), 7 deletions(-)
create mode 100644 config/fastq-screen_bowtie2.conf
rename config/{fastq-screen.conf => fastq-screen_bwa.conf} (98%)
diff --git a/config/config.yaml b/config/config.yaml
index 49b0c31..3b57aeb 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -49,13 +49,17 @@ conda:
### FASTQSCREEN --------------------------------------------------------------------------------------
fastq-screen:
- config: 'config/fastq-screen.conf' # Path to the fastq-screen configuration file
+ config: 'config/fastq-screen_bwa.conf' # Path to the fastq-screen configuration file
+ # Available options:
+ #- 'config/fastq-screen_bwa.conf' # Default fastq-screen configuration file for bwa users
+ #- 'config/fastq-screen_bowtie2.conf' # Default fastq-screen configuration file for bowtie2 users
+ #- 'config/fastq-screen_custom.conf' # Your cutom fastq-screen configuration file
subset: 10000 # Don't use whole sequences, but a subset reads (default: "1000") [INT] (0=all)
mapper: 'bwa' # Mapper used by fastq-screen for alignments (default "bwa")
# Available options:
- #- 'bwa' # Burrows-Wheeler Aligner (default, somme small genomes indexes provided, see "fastq-screen.conf")
- #- 'bowtie' # Bowtie (indexes not provided for fastq-screen)
- #- 'bowtie2' # Bowtie2 (indexes not provided for fastq-screen)
+ #- 'bwa' # Burrows-Wheeler Aligner (default, somme small genomes indexes provided, see "fastq-screen_bwa.conf")
+ #- 'bowtie2' # Bowtie2 (somme small genomes indexes provided, see "fastq-screen_bowtie2.conf")
+ #- 'bowtie' # Bowtie (indexes not provided for fastq-screen)
### BWA ----------------------------------------------------------------------------------------------
bwa:
diff --git a/config/fastq-screen_bowtie2.conf b/config/fastq-screen_bowtie2.conf
new file mode 100644
index 0000000..4cf6ccc
--- /dev/null
+++ b/config/fastq-screen_bowtie2.conf
@@ -0,0 +1,69 @@
+###I###R###D######U###2###3###3#######T###R###A###N###S###V###I###H###M###I####
+# Name ___________________ fastq-screen.conf
+# Version ________________ v.2022.11
+# Author _________________ Nicolas Fernandez
+# Affiliation ____________ IRD_TransVIHMI
+# Aim ____________________ Configuration file for Fastq-Screen (with bowtie2)
+# Date ___________________ 2021.04.30
+# Latest modifications ___ 2022.11.18
+# Use ____________________ Edit default settings (and add fasta reference)
+
+###############################################################################
+
+#### MOLECULAR BIOLOGY SEQUENCES ----------------------------------------------------------------------------
+
+### PhiX - QC_phi-X174_Coliphage_NC-001422.1
+DATABASE PhiX resources/indexes/bowtie2/QC_phi-X174_Coliphage_NC-001422-1
+### Kanamycin - Kanamycin-Resistance-Gene
+DATABASE Kanamycin resources/indexes/bowtie2/QC_Kanamycin-Resistance-Gene
+### Adapters - QC_NGS-Adapters (FastQC contaminants: www.bioinformatics.babraham.ac.uk/projects/fastqc)
+DATABASE Adapters resources/indexes/bowtie2/QC_NGS-adapters
+### Vectors - QC_UniVec_wo_PhiX_and_Kanamycin (UniVec database: http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html) without PhiX and Kanamycin
+DATABASE Vectors resources/indexes/bowtie2/QC_UniVec_wo_phiX_and_kanamycin
+
+#### TRANSVIHMI ORGANISMS -----------------------------------------------------------------------------------
+
+#### Putative Hosts (Large genomes) -----
+
+### Gorilla g4
+#DATABASE Gorilla resources/indexes/bowtie2/Gorilla_gorilla_g4
+### Chimpanzee t3
+#DATABASE Chimpanzee resources/indexes/bowtie2/Pan_troglodytes_t3
+### Human - HOST_Homo-sapiens_h38_NC-000001.11
+#DATABASE Human resources/indexes/bowtie2/HOST_Homo-sapiens_h38_NC-000001-11
+### Bat v1
+#DATABASE Bat resources/indexes/bowtie2/Pteropus_vampyrus_v1
+
+#### Main Viruses (Small genomes) -----
+
+### SARS-CoV-2 - SARS-CoV-2_Wuhan_MN908947.3
+DATABASE SARS-CoV-2 resources/indexes/bowtie2/SARS-CoV-2_Wuhan_MN908947-3
+### MPXV - Monkeypox-virus_Zaire_AF380138.1
+DATABASE Monkeypox resources/indexes/bowtie2/Monkeypox-virus_Zaire_AF380138-1
+### SPXV - Swinepox-virus_India_MW036632.1
+DATABASE Swinepox resources/indexes/bowtie2/Swinepox-virus_India_MW036632-1
+### EBOV - Ebola-virus_Zaire_AF272001.1
+DATABASE Ebola resources/indexes/bowtie2/Ebola-virus_Zaire_AF272001-1
+### HIV - HIV-1_HXB2_K03455.1
+DATABASE HIV resources/indexes/bowtie2/HIV-1_HXB2_K03455-1
+
+#### LAB MODEL ORGANISMS ------------------------------------------------------------------------------------
+
+### E. coli (Bacteria) - QC_Echerichia-coli_CP060121.1
+DATABASE Ecoli resources/indexes/bowtie2/QC_Echerichia-coli_CP060121-1
+### S. cerevisiae (Yeast) - sequence
+#DATABASE Scerevisiae resources/indexes/bowtie2/Saccharomyces_cerevisiae
+### C. elegans (Nematode) - sequence
+#DATABASE Celegans resources/indexes/bowtie2/Caenorhabditis_elegans
+### D. melanogaster (Fruit fly) - sequence
+#DATABASE Dmelanogaster resources/indexes/bowtie2/Drosophila_melanogaster
+### D. rerio (Zebrafish) - sequence
+#DATABASE Drerio resources/indexes/bowtie2/Danio_rerio
+### X. laevis (Xenope) - sequence
+#DATABASE Xlaevis resources/indexes/bowtie2/Xenopus_laevis
+### G. gallus - sequence
+#DATABASE Ggallus ressources/indexes/bowtie2/Gallus_gallus
+### Mouse m39
+#DATABASE Mouse resources/indexes/bowtie2/Mus_musculus_m39
+### Arabidopsis t10 (Plant) - sequence from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.3_TAIR10/GCF_000001735.3_TAIR10_genomic.fna.gz)
+#DATABASE Arabidopsis resources/indexes/bowtie2/Arabidopsis_thaliana_t10
diff --git a/config/fastq-screen.conf b/config/fastq-screen_bwa.conf
similarity index 98%
rename from config/fastq-screen.conf
rename to config/fastq-screen_bwa.conf
index 9b3037f..8d7780a 100644
--- a/config/fastq-screen.conf
+++ b/config/fastq-screen_bwa.conf
@@ -5,7 +5,7 @@
# Affiliation ____________ IRD_TransVIHMI
# Aim ____________________ Configuration file for Fastq-Screen (with bwa)
# Date ___________________ 2021.04.30
-# Latest modifications ___ 2022.11.10
+# Latest modifications ___ 2022.11.18
# Use ____________________ Edit default settings (and add fasta reference)
###############################################################################
diff --git a/workflow/rules/indexing_genomes.smk b/workflow/rules/indexing_genomes.smk
index fda213e..d496a05 100755
--- a/workflow/rules/indexing_genomes.smk
+++ b/workflow/rules/indexing_genomes.smk
@@ -4,7 +4,7 @@
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Snakefile with indexing genomes rules
# Date ___________________ 2022.09.28
-# Latest modifications ___ 2022.11.10
+# Latest modifications ___ 2022.11.18
# Use ____________________ snakemake -s indexing_genomes.smk --use-conda
###############################################################################
diff --git a/workflow/rules/quality_control.smk b/workflow/rules/quality_control.smk
index 568b802..f65e0cc 100755
--- a/workflow/rules/quality_control.smk
+++ b/workflow/rules/quality_control.smk
@@ -4,7 +4,7 @@
# Affiliation ____________ IRD_U233_TransVIHMI
# Aim ____________________ Snakefile with quality control rules
# Date ___________________ 2021.09.28
-# Latest modifications ___ 2022.11.10
+# Latest modifications ___ 2022.11.18
# Run ____________________ snakemake -s quality_control.smk --use-conda
###############################################################################
--
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