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workflow_templates
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updating workflow to latest program version and dependencies, pruning annotation option

master
Christiane Hassenrueck 2 months ago
parent
e5304e013c
commit
34de416ea8
18 changed files with 410 additions and 896 deletions
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  1. 18
      metaG_Illumina_PE/Snakefile
  2. 34
      metaG_Illumina_PE/config/config.yaml
  3. 22
      metaG_Illumina_PE/config/slurm_config.yaml
  4. 6
      metaG_Illumina_PE/envs/binspreader.yaml
  5. 2
      metaG_Illumina_PE/envs/busco.yaml
  6. 44
      metaG_Illumina_PE/envs/dbcan.yaml
  7. 24
      metaG_Illumina_PE/envs/megahit.yaml
  8. 12
      metaG_Illumina_PE/envs/metacoag.yaml
  9. 672
      metaG_Illumina_PE/envs/metawrap.yaml
  10. 217
      metaG_Illumina_PE/envs/phyloflash.yaml
  11. 29
      metaG_Illumina_PE/envs/spades.yaml
  12. 48
      metaG_Illumina_PE/envs/vamb.yaml
  13. 43
      metaG_Illumina_PE/rules/bin_annotation.smk
  14. 2
      metaG_Illumina_PE/rules/co_assembly.smk
  15. 54
      metaG_Illumina_PE/rules/contig_annotation.smk
  16. 26
      metaG_Illumina_PE/rules/gene_catalogue.smk
  17. 19
      metaG_Illumina_PE/rules/sample_assembly.smk
  18. 34
      metaG_Illumina_PE/rules/trimming.smk

18
metaG_Illumina_PE/Snakefile
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@ -9,7 +9,7 @@ Aim:
# specify config file
# change this path to the location of the config file with your project specific settings
configfile: "/scratch/usr/mvbchass/Repos/workflow_templates/metaG_Illumina_PE/config/config.yaml"
configfile: "/home/mvbchass/Repos/workflow_templates/metaG_Illumina_PE/config/config.yaml"
# specify wildcards for samples and paths of input file names
sample_table = pd.read_table(config["sample_list"], sep="\t", lineterminator="\n", header=None, names = ["SID", "path_R1", "path_R2"])
@ -67,12 +67,12 @@ rule all:
#counts_catalogue = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Gene_catalogue/quantified/genes_counts.txt"
# load rules
include: "rules/trimming.smk"
include: "rules/short_read.smk"
include: "rules/co_assembly.smk"
include: "rules/sample_assembly.smk"
include: "rules/final_bins.smk"
include: "rules/bin_annotation.smk"
include: "rules/contig_annotation.smk"
include: "rules/gene_catalogue.smk"
include: config["wdir"] + "/rules/trimming.smk"
include: config["wdir"] + "/rules/short_read.smk"
include: config["wdir"] + "/rules/co_assembly.smk"
include: config["wdir"] + "/rules/sample_assembly.smk"
include: config["wdir"] + "/rules/final_bins.smk"
include: config["wdir"] + "/rules/bin_annotation.smk"
include: config["wdir"] + "/rules/contig_annotation.smk"
include: config["wdir"] + "/rules/gene_catalogue.smk"

34
metaG_Illumina_PE/config/config.yaml
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@ -1,22 +1,18 @@
# Project name (will be used in the file names generated during this workflow)
project: "CombiBac_metaG"
# project: "EVAR"
# The analysis ID is a way to further structure the data in Intermediate_results and Validated_data
# e.g. in cases where multiple analyses (16S, metaG) or multiple versions of an analysis are run within the same project
analysis: "v1"
# analysis: "metaG_run1"
# Location of repository with analysis workflow
wdir: "/scratch/usr/mvbchass/Repos/workflow_templates/metaG_Illumina_PE"
wdir: "/home/mvbchass/Repos/workflow_templates/metaG_Illumina_PE"
# Name of file with sample names and sequence file locations
sample_list: "/scratch/usr/mvbchass/Repos/workflow_templates/metaG_Illumina_PE/assets/sample_list_hlrn.txt"
# sample_list: "/scratch/usr/mvbchass/Repos/workflow_templates/metaG_Illumina_PE/assets/sample_list_evar.txt"
sample_list: "/home/mvbchass/Repos/workflow_templates/metaG_Illumina_PE/assets/sample_list.txt"
# Directory for analysis data
adir: "/scratch/usr/mvbchass/Analysis_data/IOWseq000005_CombiBac"
# adir: "/scratch/usr/mvbchass/Analysis_data/IOWseq000001_EVAR_metaG"
# Default number of threads
threads: 1
@ -60,35 +56,35 @@ busco_db_dir: "/scratch/usr/mvbchass/Databases/BUSCO/20210628/busco"
gunc_db: "/scratch/usr/mvbchass/Databases/ProGenomes/v2.1/diamond/gunc_db_progenomes2.1.dmnd"
# KEGG
kegg_diamond_db: "/scratch/usr/mvbchass/Databases/KEGG/release_20221204/diamond/kegg_genes.dmnd"
kegg_mapdir: "/scratch/usr/mvbchass/Databases/KEGG/release_20221204/mapping_info"
kegg_diamond_db: "/scratch/faste/usr/mvbchass/Databases/KEGG/release_20221204/diamond/kegg_genes.dmnd"
kegg_mapdir: "/scratch/fast/usr/mvbchass/Databases/KEGG/release_20221204/mapping_info"
# Reference DB for dbCAN
dbcan_db: "/scratch/usr/mvbchass/Databases/dbCAN/v3.0.1/run_dbcan/db"
dbcan_db: "/scratch/fast/usr/mvbchass/Databases/dbCAN/v3.0.1/run_dbcan/db"
# MEROPS DB
merops_scan: "/scratch/usr/mvbchass/Databases/MEROPS/v12.1/diamond/merops_scan.dmnd"
merops_pepunit: "/scratch/usr/mvbchass/Databases/MEROPS/v12.1/diamond/merops_pepunit.dmnd"
merops_meta_pepunit: "/scratch/usr/mvbchass/Databases/MEROPS/v12.1/metadata_pepunit.txt"
merops_scan: "/scratch/fast/usr/mvbchass/Databases/MEROPS/v12.1/diamond/merops_scan.dmnd"
merops_pepunit: "/scratch/fast/usr/mvbchass/Databases/MEROPS/v12.1/diamond/merops_pepunit.dmnd"
merops_meta_pepunit: "/scratch/fast/usr/mvbchass/Databases/MEROPS/v12.1/metadata_pepunit.txt"
# TCDB
tcdb_dmnd: "/scratch/usr/mvbchass/Databases/TCDB/20220331/diamond/tcdb.dmnd"
tcdb_metadir: "/scratch/usr/mvbchass/Databases/TCDB/20220331"
tcdb_dmnd: "/scratch/fast/usr/mvbchass/Databases/TCDB/20220331/diamond/tcdb.dmnd"
tcdb_metadir: "/scratch/fast/usr/mvbchass/Databases/TCDB/20220331"
# NCycDB
ncycdb_dmnd: "/scratch/usr/mvbchass/Databases/NCycDB/2019Jul/diamond/ncycdb.dmnd"
ncycdb_metafile: "/scratch/usr/mvbchass/Databases/NCycDB/2019Jul/id2gene.map.2019Jul"
ncycdb_dmnd: "/scratch/fast/usr/mvbchass/Databases/NCycDB/2019Jul/diamond/ncycdb.dmnd"
ncycdb_metafile: "/scratch/fast/usr/mvbchass/Databases/NCycDB/2019Jul/id2gene.map.2019Jul"
# SCycDB
scycdb_dmnd: "/scratch/usr/mvbchass/Databases/SCycDB/2020Mar/diamond/scycdb.dmnd"
scycdb_metafile: "/scratch/usr/mvbchass/Databases/SCycDB/2020Mar/id2gene.map.2020Mar"
scycdb_dmnd: "/scratch/fast/usr/mvbchass/Databases/SCycDB/2020Mar/diamond/scycdb.dmnd"
scycdb_metafile: "/scratch/fast/usr/mvbchass/Databases/SCycDB/2020Mar/id2gene.map.2020Mar"
# Setting E-value and blast score ratio to filter annotations
evalue: 0.00001
bsr: 0.4
# Reference profiles for kofamscan
kofam_db: "/scratch/usr/mvbchass/Databases/KOfam/Dec2021/kofamscan"
kofam_db: "/scratch/fast/usr/mvbchass/Databases/KOfam/Dec2021/kofamscan"
# Reference database for CAT/BAT
# GTDB

22
metaG_Illumina_PE/config/slurm_config.yaml
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@ -7,7 +7,7 @@ __default__:
assembly_megahit:
time: 10080
partition: standard96
partition: large96
tasks-per-node: 1
qos: 7d
account: mvbchass
@ -21,7 +21,7 @@ co_assembly_binning:
assembly_metaspades:
time: 5760
partition: large96
partition: standard96
tasks-per-node: 1
qos: 96h
account: mvbchass
@ -34,21 +34,23 @@ single_assembly_binning:
account: mvbchass
metacoag_binning:
time: 10080
time: 5760
partition: medium40
tasks-per-node: 1
qos: 7d
qos: 96h
account: mvbchass
mapping_vamb:
time: 05:00:00
partition: standard96
prepare_vamb:
partition: medium40
vamb_binning:
time: 10080
vamb_index:
partition: medium40
vamb_binning:
time: 5760
partition: standard96
tasks-per-node: 1
qos: 7d
qos: 96h
account: mvbchass
#bin_reassembly_mapping:

6
metaG_Illumina_PE/envs/abricate.yaml → metaG_Illumina_PE/envs/binspreader.yaml
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@ -3,5 +3,7 @@ channels:
- bioconda
- defaults
dependencies:
- abricate>=1.0.1
- binspreader
- parallel
- seqkit

2
metaG_Illumina_PE/envs/busco.yaml
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@ -3,5 +3,5 @@ channels:
- bioconda
- defaults
dependencies:
- busco=5.2.2
- busco=5.4.6

44
metaG_Illumina_PE/envs/dbcan.yaml
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@ -3,45 +3,5 @@ channels:
- conda-forge
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- boost-cpp=1.74.0=h75c5d50_8
- bzip2=1.0.8=h7f98852_4
- ca-certificates=2022.10.11=h06a4308_0
- dbcan=3.0.7=pyh5e36f6f_0
- diamond=2.0.15=hb97b32f_1
- hmmer=3.3.2=h87f3376_2
- icu=70.1=h27087fc_0
- ld_impl_linux-64=2.39=hcc3a1bd_1
- libblas=3.9.0=16_linux64_openblas
- libcblas=3.9.0=16_linux64_openblas
- libffi=3.4.2=h7f98852_5
- libgcc-ng=12.2.0=h65d4601_19
- libgfortran-ng=12.2.0=h69a702a_19
- libgfortran5=12.2.0=h337968e_19
- libgomp=12.2.0=h65d4601_19
- liblapack=3.9.0=16_linux64_openblas
- libnsl=2.0.0=h7f98852_0
- libopenblas=0.3.21=pthreads_h78a6416_3
- libsqlite=3.40.0=h753d276_0
- libstdcxx-ng=12.2.0=h46fd767_19
- libuuid=2.32.1=h7f98852_1000
- libzlib=1.2.13=h166bdaf_4
- natsort=8.2.0=pyhd8ed1ab_0
- ncurses=6.3=h27087fc_1
- numpy=1.23.5=py38h7042d01_0
- openssl=3.0.7=h0b41bf4_1
- pip=22.3.1=pyhd8ed1ab_0
- prodigal=2.6.3=hec16e2b_4
- psutil=5.9.4=py38h0a891b7_0
- python=3.8.15=h4a9ceb5_0_cpython
- python_abi=3.8=3_cp38
- readline=8.2=h5eee18b_0
- scipy=1.9.3=py38h8ce737c_2
- setuptools=65.5.1=pyhd8ed1ab_0
- tk=8.6.12=h27826a3_0
- wheel=0.38.4=pyhd8ed1ab_0
- xz=5.2.8=h5eee18b_0
- zlib=1.2.13=h166bdaf_4
- zstd=1.5.2=h6239696_4
- python=3.8
- dbcan

24
metaG_Illumina_PE/envs/megahit.yaml
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@ -3,27 +3,5 @@ channels:
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- ca-certificates=2021.5.30=ha878542_0
- certifi=2021.5.30=py39hf3d152e_0
- ld_impl_linux-64=2.36.1=hea4e1c9_1
- libffi=3.3=h58526e2_2
- libgcc-ng=9.3.0=h2828fa1_19
- libgomp=9.3.0=h2828fa1_19
- libstdcxx-ng=9.3.0=h6de172a_19
- megahit=1.2.9=h2e03b76_1
- ncurses=6.2=h58526e2_4
- openssl=1.1.1k=h7f98852_0
- pip=21.1.3=pyhd8ed1ab_0
- python=3.9.6=h49503c6_1_cpython
- python_abi=3.9=2_cp39
- readline=8.1=h46c0cb4_0
- setuptools=49.6.0=py39hf3d152e_3
- sqlite=3.36.0=h9cd32fc_0
- tk=8.6.10=h21135ba_1
- tzdata=2021a=he74cb21_1
- wheel=0.36.2=pyhd3deb0d_0
- xz=5.2.5=h516909a_1
- zlib=1.2.11=h516909a_1010
- megahit

12
metaG_Illumina_PE/envs/metacoag.yaml
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@ -1,14 +1,6 @@
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- python=3.7.4
- biopython=1.74
- python-igraph=0.9.6
- fraggenescan=1.31
- hmmer=3.3.2
- networkx=2.4
- scipy=1.3.1
- numpy=1.17.2
- tqdm=4.36.1
- metacoag

672
metaG_Illumina_PE/envs/metawrap.yaml
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@ -3,340 +3,340 @@ channels:
- bioconda
- conda-forge
- defaults
- intel
dependencies:
- _libgcc_mutex=0.1=main
- _openmp_mutex=4.5=1_gnu
- _r-mutex=1.0.1=anacondar_1
- alsa-lib=1.2.3=h516909a_0
- aragorn=1.2.38=h779adbc_4
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.1=py_0
- backports_abc=0.5=py_1
- barrnap=0.9=hdfd78af_4
- bedtools=2.30.0=h7d7f7ad_1
- binutils_impl_linux-64=2.35.1=h193b22a_2
- binutils_linux-64=2.35=h67ddf6f_30
- biopython=1.68=py27_0
- blas=2.5=mkl
- blast=2.6.0=boost1.64_2
- bmfilter=3.101=hc9558a2_3
- bmtagger=3.101=h470a237_4
- bmtool=3.101=he1b5a44_3
- boost=1.64.0=py27_4
- boost-cpp=1.64.0=1
- bowtie2=2.3.5.1=py27he513fc3_0
- bwa=0.7.17=h5bf99c6_8
- bwidget=1.9.14=ha770c72_0
- bz2file=0.98=py_0
- bzip2=1.0.8=h7f98852_4
- ca-certificates=2021.5.30=ha878542_0
- cairo=1.16.0=h18b612c_1001
- certifi=2019.11.28=py27h8c360ce_1
- checkm-genome=1.0.12=py27_0
- circos=0.69.8=hdfd78af_1
- concoct=1.0.0=py27h88e4a8a_5
- curl=7.68.0=hf8cf82a_0
- cutadapt=1.18=py27h14c3975_1
- cycler=0.10.0=py_2
- cython=0.29.15=py27haf22ab1_1
- dbus=1.13.6=hfdff14a_1
- dendropy=4.5.2=pyh3252c3a_0
- expat=2.4.1=h9c3ff4c_0
- extract_fullseq=3.101=3
- fastqc=0.11.8=2
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- fontconfig=2.13.1=he4413a7_1000
- fraggenescan=1.31=h779adbc_3
- freetype=2.10.4=h0708190_1
- functools32=3.2.3.2=py_3
- futures=3.3.0=py27h8c360ce_1
- gcc_impl_linux-64=7.5.0=habd7529_19
- gcc_linux-64=7.5.0=h47867f9_30
- gettext=0.19.8.1=hf34092f_1004
- gfortran_impl_linux-64=7.5.0=h56cb351_19
- gfortran_linux-64=7.5.0=h78c8a43_30
- giflib=5.2.1=h36c2ea0_2
- glib=2.66.3=h58526e2_0
- glimmerhmm=3.0.4=pl526hf484d3e_3
- graphite2=1.3.13=h58526e2_1001
- gsl=2.5=h294904e_1
- gst-plugins-base=1.14.5=h0935bb2_2
- gstreamer=1.14.5=h36ae1b5_2
- gxx_impl_linux-64=7.5.0=hd0bb8aa_19
- gxx_linux-64=7.5.0=h555fc39_30
- harfbuzz=2.4.0=h37c48d4_1
- hmmer=3.3.2=h1b792b2_1
- icu=58.2=hf484d3e_1000
- idba=1.1.3=1
- infernal=1.1.4=h779adbc_0
- intel-openmp=2021.2.0=h06a4308_610
- jemalloc=5.2.1=h9c3ff4c_5
- joblib=0.14.1=pyh9f0ad1d_0
- jpeg=9d=h36c2ea0_0
- k8=0.2.5=h9a82719_1
- kernel-headers_linux-64=2.6.32=h77966d4_13
- kiwisolver=1.1.0=py27h9e3301b_1
- kmer-jellyfish=1.1.12=h7d875b9_1
- kraken=1.1.1=pl5262h7d875b9_5
- krb5=1.16.4=h2fd8d38_0
- krona=2.7.1=pl5262hdfd78af_6
- lcms2=2.11=hcbb858e_1
- ld_impl_linux-64=2.35.1=hea4e1c9_2
- libblas=3.8.0=5_mkl
- libboost=1.73.0=h3ff78a5_11
- libcblas=3.8.0=5_mkl
- libcurl=7.68.0=hda55be3_0
- libdeflate=1.0=h14c3975_1
- libedit=3.1.20191231=h46ee950_2
- libffi=3.2.1=he1b5a44_1007
- libgcc=7.2.0=h69d50b8_2
- libgcc-devel_linux-64=7.5.0=hda03d7c_19
- libgcc-ng=9.3.0=h5101ec6_17
- libgd=2.2.5=h0d07dcb_1005
- libgfortran-ng=7.5.0=h14aa051_19
- libgfortran4=7.5.0=h14aa051_19
- libglib=2.66.3=hbe7bbb4_0
- libgomp=9.3.0=h5101ec6_17
- libiconv=1.16=h516909a_0
- libidn11=1.34=h1cef754_0
- libidn2=2.3.1=h7f98852_0
- liblapack=3.8.0=5_mkl
- liblapacke=3.8.0=5_mkl
- libpng=1.6.37=h21135ba_2
- libssh2=1.9.0=ha56f1ee_6
- libstdcxx-devel_linux-64=7.5.0=hb016644_19
- libstdcxx-ng=9.3.0=hd4cf53a_17
- libtiff=4.1.0=hc3755c2_3
- libunistring=0.9.10=h14c3975_0
- libuuid=2.32.1=h7f98852_1000
- libwebp=1.0.2=h56121f0_5
- libxcb=1.13=h7f98852_1003
- libxml2=2.9.9=h13577e0_2
- llvm-openmp=8.0.1=hc9558a2_0
- lz4-c=1.9.3=h9c3ff4c_0
- make=4.3=hd18ef5c_1
- matplotlib=2.2.3=py27hb69df0a_0
- matplotlib-base=2.2.4=py27hfd891ef_0
- maxbin2=2.2.6=h14c3975_0
- megahit=1.1.3=py27_0
- metabat2=2.12.1=0
- minced=0.4.2=hdfd78af_1
- minimap2=2.20=h5bf99c6_0
- mkl=2019.4=243
- mmtf-python=1.0.2=py27_0
- msgpack-python=1.0.0=py27h9e3301b_1
- ncurses=6.1=hf484d3e_1002
- nose=1.3.7=py27h8c360ce_1004
- numpy=1.16.5=py27h95a1406_0
- olefile=0.46=pyh9f0ad1d_1
- openjdk=11.0.8=hacce0ff_0
- openmp=8.0.1=0
- openssl=1.1.1k=h7f98852_0
- pandas=0.24.2=py27hb3f55d8_0
- pango=1.40.14=he7ab937_1005
- parallel=20160622=1
- patsy=0.5.1=py_0
- pcre=8.45=h9c3ff4c_0
- perl=5.26.2=h36c2ea0_1008
- perl-app-cpanminus=1.7044=pl526_1
- perl-autoloader=5.74=pl526_2
- perl-base=2.23=pl526_1
- perl-bioperl=1.6.924=4
- perl-business-isbn=3.004=pl526_0
- perl-business-isbn-data=20140910.003=pl526_0
- perl-carp=1.38=pl526_3
- perl-clone=0.42=pl526h516909a_0
- perl-compress-raw-zlib=2.087=pl526hc9558a2_0
- perl-config-general=2.63=pl526_0
- perl-constant=1.33=pl526_1
- perl-data-dumper=2.173=pl526_0
- perl-digest-hmac=1.03=pl526_3
- perl-digest-md5=2.55=pl526_0
- perl-digest-perl-md5=1.9=pl526_1
- perl-dynaloader=1.25=pl526_1
- perl-encode=2.88=pl526_1
- perl-encode-locale=1.05=pl526_6
- perl-exporter=5.72=pl526_1
- perl-exporter-tiny=1.002001=pl526_0
- perl-extutils-makemaker=7.36=pl526_1
- perl-file-listing=6.04=pl526_1
- perl-file-path=2.16=pl526_0
- perl-file-temp=0.2304=pl526_2
- perl-font-ttf=1.06=pl526_0
- perl-gd=2.71=pl526he860b03_0
- perl-html-parser=3.72=pl526h6bb024c_5
- perl-html-tagset=3.20=pl526_3
- perl-http-cookies=6.04=pl526_0
- perl-http-daemon=6.01=pl526_1
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metaG_Illumina_PE/envs/phyloflash.yaml
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channels:
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dependencies:
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- blas=1.1=openblas
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- certifi=2020.6.20=pyhd3eb1b0_3
- cffi=1.14.0=py27hd463f26_0
- chardet=3.0.4=py27h8c360ce_1006
- colorama=0.4.4=pyh9f0ad1d_0
- conda=4.8.4=py27_0
- conda-package-handling=1.6.0=py27hdf8410d_2
- cryptography=2.8=py27h2c19f6a_2
- curl=7.76.1=h979ede3_1
- emirge=0.61.1=py27h59c9234_6
- enum34=1.1.10=py27h8c360ce_1
- fontconfig=2.13.1=hba837de_1005
- freetype=2.10.4=h0708190_1
- fribidi=1.0.10=h36c2ea0_0
- futures=3.3.0=py27h8c360ce_1
- gcc_impl_linux-64=9.4.0=h03d3576_8
- gcc_linux-64=9.4.0=h391b98a_0
- gettext=0.19.8.1=hf34092f_1004
- gfortran_impl_linux-64=9.4.0=h0003116_8
- gfortran_linux-64=9.4.0=hf0ab688_0
- giflib=5.2.1=h36c2ea0_2
- graphite2=1.3.13=h58526e2_1001
- gsl=2.6=he838d99_2
- gxx_impl_linux-64=9.4.0=h03d3576_8
- gxx_linux-64=9.4.0=h0316aca_0
- harfbuzz=2.7.2=ha5b49bf_1
- htslib=1.12=h9093b5e_1
- icu=67.1=he1b5a44_0
- idna=2.10=pyh9f0ad1d_0
- ipaddress=1.0.23=py_0
- jbig=2.1=h7f98852_2003
- jpeg=9d=h36c2ea0_0
- kernel-headers_linux-64=2.6.32=he073ed8_14
- krb5=1.17.2=h926e7f8_0
- lcms2=2.12=hddcbb42_0
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- lerc=2.2.1=h9c3ff4c_0
- libblas=3.9.0=1_h86c2bf4_netlib
- libcblas=3.9.0=5_h92ddd45_netlib
- libcurl=7.76.1=hc4aaa36_1
- libdeflate=1.7=h7f98852_5
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=h516909a_1
- libffi=3.2.1=he1b5a44_1007
- libgcc-devel_linux-64=9.4.0=hd854feb_8
- libgcc-ng=11.1.0=hc902ee8_8
- libgfortran=3.0.0=1
- libgfortran-ng=11.1.0=h69a702a_8
- libgfortran5=11.1.0=h6c583b3_8
- libglib=2.66.3=hbe7bbb4_0
- libgomp=11.1.0=hc902ee8_8
- libiconv=1.16=h516909a_0
- liblapack=3.9.0=5_h92ddd45_netlib
- libnghttp2=1.43.0=h812cca2_0
- libpng=1.6.37=h21135ba_2
- libsanitizer=9.4.0=h79bfe98_8
- libsolv=0.7.19=h780b84a_5
- libssh2=1.9.0=ha56f1ee_6
- libstdcxx-devel_linux-64=9.4.0=hd854feb_8
- libstdcxx-ng=11.1.0=h56837e0_8
- libtiff=4.3.0=hf544144_1
- libuuid=2.32.1=h7f98852_1000
- libwebp-base=1.2.1=h7f98852_0
- libxcb=1.13=h7f98852_1003
- libxml2=2.9.10=h68273f3_2
- llvm-openmp=8.0.1=hc9558a2_0
- lz4-c=1.9.3=h9c3ff4c_1
- mafft=7.487=h779adbc_0
- make=4.3=hd18ef5c_1
- mamba=0.1.0=py27hc9558a2_2
- mmtf-python=1.0.2=py27_0
- msgpack-python=1.0.0=py27h9e3301b_1
- ncurses=6.2=h58526e2_4
- numpy=1.16.5=py27h95a1406_0
- olefile=0.46=pyh9f0ad1d_1
- openblas=0.3.3=ha44fe06_1
- openjdk=11.0.8=hacce0ff_0
- openmp=8.0.1=0
- openssl=1.1.1k=h7f98852_1
- pango=1.42.4=h69149e4_5
- pbzip2=1.1.13=0
- pcre=8.45=h9c3ff4c_0
- pcre2=10.36=h032f7d1_1
- perl=5.32.1=0_h7f98852_perl5
- phyloflash=3.4=hdfd78af_1
- pigz=2.6=h27826a3_0
- pillow=6.2.1=py27hd70f55b_1
- pip=20.1.1=pyh9f0ad1d_0
- pixman=0.40.0=h36c2ea0_0
- pthread-stubs=0.4=h36c2ea0_1001
- pycosat=0.6.3=py27hdf8410d_1004
- pycparser=2.20=pyh9f0ad1d_2
- pyopenssl=20.0.1=pyhd3eb1b0_1
- pysam=0.16.0.1=py27hc729bab_3
- pysocks=1.7.1=py27h8c360ce_1
- python=2.7.15=h5a48372_1011_cpython
- python_abi=2.7=1_cp27mu
- r-assertthat=0.2.1=r40hc72bb7e_2
- r-backports=1.2.1=r40hcfec24a_0
- r-base=4.0.3=ha43b4e8_3
- r-brio=1.1.2=r40hcfec24a_0
- r-callr=3.7.0=r40hc72bb7e_0
- r-cli=3.0.1=r40h03ef668_1
- r-colorspace=2.0_2=r40hcfec24a_0
- r-crayon=1.4.1=r40hc72bb7e_0
- r-desc=1.3.0=r40hc72bb7e_0
- r-diffobj=0.3.4=r40hcfec24a_0
- r-digest=0.6.27=r40h03ef668_0
- r-ellipsis=0.3.2=r40hcfec24a_0
- r-evaluate=0.14=r40hc72bb7e_2
- r-fansi=0.5.0=r40hcfec24a_0
- r-farver=2.1.0=r40h03ef668_0
- r-getopt=1.20.3=r40ha770c72_2
- r-ggdendro=0.1.22=r40hc72bb7e_0
- r-ggplot2=3.3.5=r40hc72bb7e_0
- r-glue=1.4.2=r40hcfec24a_0
- r-gtable=0.3.0=r40hc72bb7e_3
- r-isoband=0.2.5=r40h03ef668_0
- r-jsonlite=1.7.2=r40hcfec24a_0
- r-labeling=0.4.2=r40hc72bb7e_0
- r-lattice=0.20_44=r40hcfec24a_0
- r-lifecycle=1.0.0=r40hc72bb7e_0
- r-magrittr=2.0.1=r40hcfec24a_1
- r-mass=7.3_54=r40hcfec24a_0
- r-matrix=1.3_4=r40he454529_0
- r-mgcv=1.8_36=r40he454529_0
- r-munsell=0.5.0=r40hc72bb7e_1003
- r-nlme=3.1_152=r40h859d828_0
- r-optparse=1.6.6=r40hc72bb7e_1
- r-pillar=1.6.2=r40hc72bb7e_0
- r-pkgconfig=2.0.3=r40hc72bb7e_1
- r-pkgload=1.2.1=r40h03ef668_0
- r-plyr=1.8.6=r40h03ef668_1
- r-praise=1.0.0=r40hc72bb7e_1004
- r-processx=3.5.2=r40hcfec24a_0
- r-ps=1.6.0=r40hcfec24a_0
- r-r6=2.5.1=r40hc72bb7e_0
- r-rcolorbrewer=1.1_2=r40h785f33e_1003
- r-rcpp=1.0.7=r40h03ef668_0
- r-rematch2=2.1.2=r40hc72bb7e_1
- r-reshape2=1.4.4=r40h03ef668_1
- r-rlang=0.4.11=r40hcfec24a_0
- r-rprojroot=2.0.2=r40hc72bb7e_0
- r-rstudioapi=0.13=r40hc72bb7e_0
- r-scales=1.1.1=r40hc72bb7e_0
- r-stringi=1.5.3=r40hca8494e_0
- r-stringr=1.4.0=r40hc72bb7e_2
- r-testthat=3.0.4=r40h03ef668_0
- r-tibble=3.1.3=r40hcfec24a_0
- r-utf8=1.2.2=r40hcfec24a_0
- r-vctrs=0.3.8=r40hcfec24a_1
- r-viridislite=0.4.0=r40hc72bb7e_0
- r-waldo=0.3.0=r40hc72bb7e_0
- r-withr=2.4.2=r40hc72bb7e_0
- readline=8.1=h46c0cb4_0
- reportlab=3.5.42=py27heca39a3_0
- requests=2.25.1=pyhd3deb0d_0
- ruamel_yaml=0.15.80=py27hdf8410d_1001
- samtools=1.12=h9aed4be_1
- scandir=1.10.0=py27hdf8410d_1
- scipy=1.2.0=py27_blas_openblashb06ca3d_200
- sed=4.8=he412f7d_0
- setuptools=44.0.0=py27_0
- six=1.16.0=pyh6c4a22f_0
- sortmerna=2.1b=he860b03_4
- spades=3.14.1=h95f258a_2
- sqlite=3.36.0=h9cd32fc_0
- sysroot_linux-64=2.12=he073ed8_14
- tk=8.6.11=h21135ba_0
- tktable=2.10=hb7b940f_3
- tqdm=4.62.2=pyhd8ed1ab_0
- urllib3=1.26.6=pyhd8ed1ab_0
- vsearch=2.17.1=h95f258a_0
- wheel=0.37.0=pyhd8ed1ab_1
- xorg-fixesproto=5.0=h7f98852_1002
- xorg-inputproto=2.3.2=h7f98852_1002
- xorg-kbproto=1.0.7=h7f98852_1002
- xorg-libice=1.0.10=h7f98852_0
- xorg-libsm=1.2.3=hd9c2040_1000
- xorg-libx11=1.7.2=h7f98852_0
- xorg-libxau=1.0.9=h7f98852_0
- xorg-libxdmcp=1.1.3=h7f98852_0
- xorg-libxext=1.3.4=h7f98852_1
- xorg-libxfixes=5.0.3=h7f98852_1004
- xorg-libxi=1.7.10=h7f98852_0
- xorg-libxrender=0.9.10=h7f98852_1003
- xorg-libxt=1.2.1=h7f98852_2
- xorg-libxtst=1.2.3=h7f98852_1002
- xorg-recordproto=1.14.2=h7f98852_1002
- xorg-renderproto=0.11.1=h7f98852_1002
- xorg-xextproto=7.3.0=h7f98852_1002
- xorg-xproto=7.0.31=h7f98852_1007
- xz=5.2.5=h516909a_1
- yaml=0.2.5=h516909a_0
- zlib=1.2.11=h516909a_1010
- zstd=1.5.0=ha95c52a_0
- phyloflash
- sortmerna=2.1b

29
metaG_Illumina_PE/envs/spades.yaml
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@ -3,32 +3,5 @@ channels:
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- _sysroot_linux-64_curr_repodata_hack=3=h5bd9786_12
- bzip2=1.0.8=h7f98852_4
- ca-certificates=2021.5.30=ha878542_0
- kernel-headers_linux-64=3.10.0=h4a8ded7_12
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- libffi=3.3=h58526e2_2
- libgcc-ng=11.1.0=hc902ee8_8
- libgomp=11.1.0=hc902ee8_8
- libstdcxx-ng=11.1.0=h56837e0_8
- llvm-openmp=8.0.1=hc9558a2_0
- ncurses=6.2=h58526e2_4
- openmp=8.0.1=0
- openssl=1.1.1k=h7f98852_1
- pip=21.2.4=pyhd8ed1ab_0
- python=3.9.6=h49503c6_1_cpython
- python_abi=3.9=2_cp39
- readline=8.1=h46c0cb4_0
- setuptools=57.4.0=py39hf3d152e_0
- spades=3.15.3=h95f258a_0
- sqlite=3.36.0=h9cd32fc_0
- sysroot_linux-64=2.17=h4a8ded7_12
- tk=8.6.11=h21135ba_0
- tzdata=2021a=he74cb21_1
- wheel=0.37.0=pyhd8ed1ab_1
- xz=5.2.5=h516909a_1
- zlib=1.2.11=h516909a_1010
- spades

48
metaG_Illumina_PE/envs/vamb.yaml
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@ -3,51 +3,5 @@ channels:
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_llvm
- bzip2=1.0.8=h7f98852_4
- c-ares=1.17.2=h7f98852_0
- ca-certificates=2021.7.5=h06a4308_1
- cffi=1.14.6=py37h036bc23_1
- future=0.18.2=py37h89c1867_3
- krb5=1.19.2=hcc1bbae_2
- ld_impl_linux-64=2.36.1=hea4e1c9_2
- libblas=3.9.0=11_linux64_mkl
- libcblas=3.9.0=11_linux64_mkl
- libcurl=7.79.1=h2574ce0_1
- libdeflate=1.7=h7f98852_5
- libedit=3.1.20210714=h7f8727e_0
- libev=4.33=h516909a_1
- libffi=3.4.2=h9c3ff4c_4
- libgcc-ng=11.2.0=h1d223b6_9
- liblapack=3.9.0=11_linux64_mkl
- libnghttp2=1.43.0=h812cca2_1
- libprotobuf=3.16.0=h780b84a_0
- libssh2=1.10.0=ha56f1ee_2
- libstdcxx-ng=11.2.0=he4da1e4_9
- libzlib=1.2.11=h36c2ea0_1013
- llvm-openmp=12.0.1=h4bd325d_1
- mkl=2021.3.0=h726a3e6_557
- ncurses=6.2=h58526e2_4
- ninja=1.10.2=h4bd325d_1
- numpy=1.21.2=py37h31617e3_0
- openssl=1.1.1l=h7f98852_0
- pip=21.2.4=pyhd8ed1ab_0
- pycparser=2.20=pyh9f0ad1d_2
- pysam=0.17.0=py37h45aed0b_0
- python=3.7.10=hb7a2778_101_cpython
- python_abi=3.7=2_cp37m
- pytorch=1.9.0=cpu_py37hb06efa0_2
- pytorch-cpu=1.9.0=cpu_py37h718b53a_2
- readline=8.1=h46c0cb4_0
- setuptools=58.0.4=py37h89c1867_2
- sleef=3.5.1=h9b69904_2
- sqlite=3.36.0=h9cd32fc_2
- tbb=2021.3.0=h4bd325d_0
- tk=8.6.11=h27826a3_1
- typing_extensions=3.10.0.2=pyha770c72_0
- vamb=3.0.2=py37h73a75cf_1
- wheel=0.37.0=pyhd8ed1ab_1
- xz=5.2.5=h516909a_1
- zlib=1.2.11=h36c2ea0_1013
- vamb

43
metaG_Illumina_PE/rules/bin_annotation.smk
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@ -143,23 +143,6 @@ rule metaerg_annotation:
rm -rf tmp/
"""
rule interproscan_metaerg:
input:
cds = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/metaerg_out/{bin}/data/cds.faa"
output:
ipr = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/metaerg_out/{bin}/data/iprout.tsv"
params:
prefix = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/metaerg_out/{bin}/data/iprout",
tmpdir = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/metaerg_out/{bin}/ipr_tmp"
threads: config["annotation_threads"]
log: config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/metaerg_out/logs/{bin}_interproscan.log"
shell:
"""
interproscan.sh -i {input.cds} -b {params.prefix} -goterms -cpu {threads} -T {params.tmpdir} -f TSV >> {log} 2>&1
sed -i '1i feature_id\tseq_md5\tseq_len\tanalysis\tsignature_accession\tsignature_description\tstart\tend\tscore\tstatus\tdate_run\tipr_accession\tipr_description\tgo_terms' {output.ipr}
rm -rf {params.tmpdir}
"""
rule kegg_metaerg:
input:
cds = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/metaerg_out/{bin}/data/cds.faa"
@ -378,40 +361,16 @@ rule kofam_metaerg:
rm -rf {params.tmpdir}
"""
# rule abricate_bins:
# input:
# fasta = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_final/bins/{bin}.fa"
# output:
# abricate_out = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/abricate_out/{bin}/out_abricate.txt"
# params:
# outdir = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/abricate_out/{bin}"
# threads: config["annotation_threads"]
# conda: config["wdir"] + "/envs/abricate.yaml"
# shell:
# """
# mkdir -p {params.outdir}
# echo -e "FILE\\tSEQUENCE\\tSTART\\tEND\\tSTRAND\\tGENE\\tCOVERAGE\\tCOVERAGE_MAP\\tGAPS\\t%COVERAGE\\t%IDENTITY\\tDATABASE\\tACCESSION\\tPRODUCT\\tRESISTANCE" > {output.abricate_out}
# ARGDB="argannot card megares ncbi plasmidfinder resfinder vfdb"
# for i in $ARGDB
# do
# abricate --db $i --threads {threads} --quiet {input.fasta} > {params.outdir}/tmp.txt
# sed '1d' {params.outdir}/tmp.txt >> {output.abricate_out}
# rm {params.outdir}/tmp.txt
# done
# """
rule parse_annotation:
input:
metaerg = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/metaerg_out/{bin}/data/master.tsv.txt",
# ipr = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/metaerg_out/{bin}/data/iprout.tsv",
kegg = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/kegg_out/{bin}/out_kegg_parsed_best.txt",
dbcan = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/dbcan_out/{bin}/overview.txt",
merops = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/merops_out/{bin}/out_merops_parsed_best.txt",
tcdb = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/tcdb_out/{bin}/out_tcdb_parsed_best.txt",
ncycdb = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/ncycdb_out/{bin}/out_ncycdb_parsed_best.txt",
scycdb = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/scycdb_out/{bin}/out_scycdb_parsed_best.txt",
kofam = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/kofam_out/{bin}/out_kofam_parsed.txt",
abricate = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/abricate_out/{bin}/out_abricate.txt"
kofam = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/kofam_out/{bin}/out_kofam_parsed.txt"
output:
txt = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Bin_annotation/summaries/{bin}_annotation_summary.txt"
params:

2
metaG_Illumina_PE/rules/co_assembly.smk
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@ -13,7 +13,7 @@ rule assembly_megahit:
"""
echo "{input.clean_R1}" | tr ' ' ',' > {params.outdir}/R1.csv
echo "{input.clean_R2}" | tr ' ' ',' > {params.outdir}/R2.csv
megahit --presets meta-sensitive -1 $(<{params.outdir}/R1.csv) -2 $(<{params.outdir}/R2.csv) -t {threads} -m 0.9 --min-contig-len 1000 --continue -o {params.outdir}/megahit_metasensitive/tmp > {log} 2>&1
megahit --presets meta-sensitive -1 $(<{params.outdir}/R1.csv) -2 $(<{params.outdir}/R2.csv) -t {threads} -m 0.98 --min-contig-len 1000 --continue -o {params.outdir}/megahit_metasensitive/tmp > {log} 2>&1
mv {params.outdir}/megahit_metasensitive/tmp/* {params.outdir}/megahit_metasensitive/
"""

54
metaG_Illumina_PE/rules/contig_annotation.smk
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@ -89,22 +89,6 @@ checkpoint split_contigs:
sed '/^\\#\\#FASTA$/,$d' {input.gff} > {output.gff}
"""
rule interproscan_contigs:
input:
cds = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/tmp_split/splits/{split}.faa"
output:
ipr = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/tmp_split/ipr_out/{split}_iprout.tsv"
params:
prefix = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/tmp_split/ipr_out/{split}_iprout",
tmpdir = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/tmp_split/ipr_out/tmp_ipr_{split}"
threads: config["annotation_threads"]
log: config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/tmp_split/ipr_out/logs/{split}_interproscan.log"
shell:
"""
interproscan.sh -i {input.cds} -b {params.prefix} -goterms -cpu {threads} -T {params.tmpdir} -f TSV >> {log} 2>&1
rm -rf {params.tmpdir}
"""
rule merops_contigs:
input:
cds = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/metaerg_out/data/cds.faa"
@ -252,34 +236,6 @@ rule kofam_contigs:
rm -rf {params.tmpdir}
"""
# rule abricate_contigs:
# input:
# fasta = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Co_assembly/megahit_metasensitive/final_assembly.fa"
# output:
# abricate_out = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/abricate_out/out_abricate.txt"
# params:
# outdir = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/abricate_out"
# threads: config["parallel_threads"]
# conda: config["wdir"] + "/envs/abricate.yaml"
# shell:
# """
# mkdir -p {params.outdir}
# echo -e "FILE\\tSEQUENCE\\tSTART\\tEND\\tSTRAND\\tGENE\\tCOVERAGE\\tCOVERAGE_MAP\\tGAPS\\t%COVERAGE\\t%IDENTITY\\tDATABASE\\tACCESSION\\tPRODUCT\\tRESISTANCE" > {output.abricate_out}
# ARGDB="argannot card megares ncbi plasmidfinder resfinder vfdb"
# for i in $ARGDB
# do
# abricate --db $i --threads {threads} --quiet {input.fasta} > {params.outdir}/tmp.txt
# sed '1d' {params.outdir}/tmp.txt >> {output.abricate_out}
# rm {params.outdir}/tmp.txt
# done
# """
def aggregate_ipr_splits(wildcards):
checkpoint_output = checkpoints.split_contigs.get().output['split_dir']
fasta_files = sorted(glob.glob(os.path.join(checkpoint_output, '*.faa')))
split = [re.sub('\.faa$', '', os.path.basename(x)) for x in fasta_files]
return expand(config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/tmp_split/ipr_out/{split}_iprout.tsv", split = split)
def aggregate_dbcan_splits(wildcards):
checkpoint_output = checkpoints.split_contigs.get().output['split_dir']
fasta_files = sorted(glob.glob(os.path.join(checkpoint_output, '*.faa')))
@ -288,15 +244,11 @@ def aggregate_dbcan_splits(wildcards):
rule collect_contig_splits:
input:
ipr = aggregate_ipr_splits,
dbcan = aggregate_dbcan_splits
output:
ipr = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/metaerg_out/data/iprout.tsv",
dbcan = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/dbcan_out/overview.txt"
shell:
"""
cat {input.ipr} > {output.ipr}
sed -i '1i feature_id\tseq_md5\tseq_len\tanalysis\tsignature_accession\tsignature_description\tstart\tend\tscore\tstatus\tdate_run\tipr_accession\tipr_description\tgo_terms' {output.ipr}
echo -e "Gene ID\\tEC#\\tHMMER\\teCAMI\\tDIAMOND\\t#ofTools" > {output.dbcan}
for i in {input.dbcan}
do
@ -308,13 +260,11 @@ rule summarize_annotation_contigs:
input:
metaerg = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/metaerg_out/data/master.tsv.txt",
dbcan = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/dbcan_out/overview.txt",
ipr = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/metaerg_out/data/iprout.tsv",
kegg = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/kegg_out/out_kegg_parsed_best.txt",
merops = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/merops_out/out_merops_parsed_best.txt",
tcdb = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/tcdb_out/out_tcdb_parsed_best.txt",
ncycdb = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/ncycdb_out/out_ncycdb_parsed_best.txt",
kofam = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/kofam_out/out_kofam_parsed.txt",
# abricate = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/abricate_out/out_abricate.txt"
kofam = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/kofam_out/out_kofam_parsed.txt"
output:
rds = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/annotation_summary.rds",
txt = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Contig_annotation/annotation_summary.txt"
@ -325,7 +275,7 @@ rule summarize_annotation_contigs:
shell:
"""
sed 's/\\t$//' {input.metaerg} > {params.outdir}/tmp_metaerg.txt
{params.script} -m {params.outdir}/tmp_metaerg.txt -i {input.ipr} -p {input.merops} -t {input.tcdb} -d {input.dbcan} -n {input.ncycdb} -k {input.kegg} -K {input.kofam} -o {params.outdir}/annotation_summary
{params.script} -m {params.outdir}/tmp_metaerg.txt -p {input.merops} -t {input.tcdb} -d {input.dbcan} -n {input.ncycdb} -k {input.kegg} -K {input.kofam} -o {params.outdir}/annotation_summary
rm {params.outdir}/tmp_metaerg.txt
"""

26
metaG_Illumina_PE/rules/gene_catalogue.smk
Unescape View File

@ -267,22 +267,6 @@ checkpoint split_gene_catalogue:
seqkit split2 -1 {input.cluster_filt} -p 100 -O splits -f
"""
rule interproscan_gene_catalogue:
input:
cds = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Gene_catalogue/tmp_split/splits/{split}.faa"
output:
ipr = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Gene_catalogue/tmp_split/ipr_out/{split}_iprout.tsv"
params:
prefix = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Gene_catalogue/tmp_split/ipr_out/{split}_iprout",
tmpdir = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Gene_catalogue/tmp_split/ipr_out/tmp_ipr_{split}"
threads: config["annotation_threads"]
log: config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Gene_catalogue/tmp_split/ipr_out/logs/{split}_interproscan.log"
shell:
"""
interproscan.sh -i {input.cds} -b {params.prefix} -goterms -cpu {threads} -T {params.tmpdir} -f TSV >> {log} 2>&1
rm -rf {params.tmpdir}
"""
rule dbcan_gene_catalogue:
input:
cds = config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Gene_catalogue/tmp_split/splits/{split}.faa",
@ -305,12 +289,6 @@ rule dbcan_gene_catalogue:
rm {params.split}.gff
"""
def aggregate_ipr_splits_gene_catalogue(wildcards):
checkpoint_output = checkpoints.split_gene_catalogue.get().output['split_dir']
fasta_files = sorted(glob.glob(os.path.join(checkpoint_output, '*.faa')))
split = [re.sub('\.faa$', '', os.path.basename(x)) for x in fasta_files]
return expand(config["adir"] + "/Intermediate_results/" + config["analysis"] + "/Gene_catalogue/tmp_split/ipr_out/{split}_iprout.tsv", split = split)
def aggregate_dbcan_splits_gene_catalogue(wildcards):
checkpoint_output = checkpoints.split_contigs.get().output['split_dir']
fasta_files = sorted(glob.glob(os.path.join(checkpoint_output, '*.faa')))
@ -319,15 +297,11 @@ def aggregate_dbcan_splits_gene_catalogue(wildcards):