Sync updates from master into branch

GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv

@@ -11,7 +11,7 @@ ECOLI,Escherichia coli,str. K-12 substr. MG1655,59,ensembl_bacteria,https://ftp.
 HUMAN,Homo sapiens,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz,9606,org.Hs.eg.db,,https://figshare.com/ndownloader/files/48354445,https://figshare.com/ndownloader/files/48354448
 ,Lactobacillus acidophilus,NCFM,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/985/GCF_000011985.1_ASM1198v1/GCF_000011985.1_ASM1198v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/985/GCF_000011985.1_ASM1198v1/GCF_000011985.1_ASM1198v1_genomic.gtf.gz,272621,,,https://figshare.com/ndownloader/files/49061254,https://figshare.com/ndownloader/files/49061257
 MOUSE,Mus musculus,,112,ensembl,https://ftp.ensembl.org/pub/release-112/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz,https://ftp.ensembl.org/pub/release-112/gtf/mus_musculus/Mus_musculus.GRCm39.112.gtf.gz,10090,org.Mm.eg.db,,https://figshare.com/ndownloader/files/48354460,https://figshare.com/ndownloader/files/48354457
-,Mycobacterium marinum,M,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,216594,,,https://figshare.com/ndownloader/files/49061260,https://figshare.com/ndownloader/files/49061263
+,Mycobacterium marinum,M,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/018/345/GCF_000018345.1_ASM1834v1/GCF_000018345.1_ASM1834v1_genomic.gtf.gz,216594,,,https://figshare.com/ndownloader/files/49061260,https://figshare.com/ndownloader/files/49061263
 ORYSJ,Oryza sativa,Japonica,59,ensembl_plants,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.dna.toplevel.fa.gz,https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-59/gtf/oryza_sativa/Oryza_sativa.IRGSP-1.0.59.gtf.gz,39947,,,https://figshare.com/ndownloader/files/48354451,https://figshare.com/ndownloader/files/48354454
 ORYLA,Oryzias latipes,,112,ensembl,http://ftp.ensembl.org/pub/release-112/fasta/oryzias_latipes/dna/Oryzias_latipes.ASM223467v1.dna.toplevel.fa.gz,http://ftp.ensembl.org/pub/release-112/gtf/oryzias_latipes/Oryzias_latipes.ASM223467v1.112.gtf.gz,8090,,org.Olatipes.eg.db,https://figshare.com/ndownloader/files/48354463,https://figshare.com/ndownloader/files/48354466
 ,Pseudomonas aeruginosa,UCBPP-PA14,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/014/625/GCF_000014625.1_ASM1462v1/GCF_000014625.1_ASM1462v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/014/625/GCF_000014625.1_ASM1462v1/GCF_000014625.1_ASM1462v1_genomic.gtf.gz,208963,,,https://figshare.com/ndownloader/files/49061266,https://figshare.com/ndownloader/files/49061269
@@ -21,4 +21,5 @@ SALTY,Salmonella enterica,serovar Typhimurium str. LT2,,ncbi,https://ftp.ncbi.nl
 ,Serratia liquefaciens,ATCC 27592,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/085/GCF_000422085.1_ASM42208v1/GCF_000422085.1_ASM42208v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/422/085/GCF_000422085.1_ASM42208v1/GCF_000422085.1_ASM42208v1_genomic.gtf.gz,1346614,,,https://figshare.com/ndownloader/files/49061278,https://figshare.com/ndownloader/files/49061281
 ,Staphylococcus aureus,MRSA252,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/505/GCF_000011505.1_ASM1150v1/GCF_000011505.1_ASM1150v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/505/GCF_000011505.1_ASM1150v1/GCF_000011505.1_ASM1150v1_genomic.gtf.gz,282458,,,https://figshare.com/ndownloader/files/49061284,https://figshare.com/ndownloader/files/49061287
 ,Streptococcus mutans,UA159,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/465/GCF_000007465.2_ASM746v2/GCF_000007465.2_ASM746v2_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/007/465/GCF_000007465.2_ASM746v2/GCF_000007465.2_ASM746v2_genomic.gtf.gz,210007,,,https://figshare.com/ndownloader/files/49061290,https://figshare.com/ndownloader/files/49061293
-,Vibrio fischeri,ES114,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/805/GCF_000011805.1_ASM1180v1/GCF_000011805.1_ASM1180v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/805/GCF_000011805.1_ASM1180v1/GCF_000011805.1_ASM1180v1_genomic.gtf.gz,312309,,,https://figshare.com/ndownloader/files/49061296,https://figshare.com/ndownloader/files/49061299
+
+,Vibrio fischeri,ES114,,ncbi,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/805/GCF_000011805.1_ASM1180v1/GCF_000011805.1_ASM1180v1_genomic.fna.gz,https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/011/805/GCF_000011805.1_ASM1180v1/GCF_000011805.1_ASM1180v1_genomic.gtf.gz,312309,,,https://figshare.com/ndownloader/files/49061296,https://figshare.com/ndownloader/files/49061299

Metagenomics/Illumina/Workflow_Documentation/NF_MGIllumina/workflow_code/envs/humann3.yaml

@@ -1,8 +1,7 @@
 channels:
     - conda-forge
     - bioconda
-    - defaults
     - biobakery
 dependencies:
     - humann=3.9
-    - metaphlan=4.10
+    - metaphlan=4.1.0