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Updated modules and subworkflows
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GallVp committed Aug 23, 2024
1 parent 2baea7f commit e94e37c
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24 changes: 12 additions & 12 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,12 @@
"gallvp": {
"agat/spaddintrons": {
"branch": "main",
"git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130",
"git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d",
"installed_by": ["gxf_fasta_agat_spaddintrons_spextractsequences"]
},
"agat/spextractsequences": {
"branch": "main",
"git_sha": "7bf6fbca23edc94490ffa6709f52b2f71c6fb130",
"git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d",
"installed_by": ["gxf_fasta_agat_spaddintrons_spextractsequences"]
},
"braker3": {
Expand All @@ -22,22 +22,22 @@
},
"busco/busco": {
"branch": "main",
"git_sha": "ab92c438688c1f4a3753b65914bfd2e6319cebb2",
"git_sha": "0fcdaa66410acee08d31884cdc3e8e4b1b79e66a",
"installed_by": ["fasta_gxf_busco_plot"]
},
"busco/generateplot": {
"branch": "main",
"git_sha": "ab92c438688c1f4a3753b65914bfd2e6319cebb2",
"git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d",
"installed_by": ["fasta_gxf_busco_plot"]
},
"custom/restoregffids": {
"branch": "main",
"git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
"git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d",
"installed_by": ["fasta_edta_lai"]
},
"custom/shortenfastaids": {
"branch": "main",
"git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
"git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d",
"installed_by": ["fasta_edta_lai"]
},
"edta/edta": {
Expand All @@ -47,17 +47,17 @@
},
"gffread": {
"branch": "main",
"git_sha": "c04bf39d67027e044a6eaed0b7b0439fd8866fc7",
"git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d",
"installed_by": ["fasta_gxf_busco_plot"]
},
"ltrretriever/lai": {
"branch": "main",
"git_sha": "490f8ab54c632d84f99edd6f208305ac5e283ab3",
"git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d",
"installed_by": ["fasta_edta_lai"]
},
"repeatmasker/repeatmasker": {
"branch": "main",
"git_sha": "07c6fda11aff03d2d7fc68224e7fd96866fc6a8f",
"git_sha": "004aba06875a2fee13207e2ffaa04deb2190a35d",
"installed_by": ["modules"]
}
}
Expand Down Expand Up @@ -132,7 +132,7 @@
},
"fastqc": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"gffcompare": {
Expand Down Expand Up @@ -168,12 +168,12 @@
},
"repeatmodeler/builddatabase": {
"branch": "master",
"git_sha": "1cbb5551b917aa423e414dcd69898d01520a309d",
"git_sha": "52507581f62929f98dd6e6c5c5824583fa6ef94d",
"installed_by": ["modules"]
},
"repeatmodeler/repeatmodeler": {
"branch": "master",
"git_sha": "84efd2f87d07deb22ee9378f065a9aa5f1434161",
"git_sha": "52507581f62929f98dd6e6c5c5824583fa6ef94d",
"installed_by": ["modules"]
},
"samtools/cat": {
Expand Down
2 changes: 1 addition & 1 deletion modules/gallvp/agat/spaddintrons/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,6 @@ name: "agat_spaddintrons"
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- "bioconda::agat=1.4.0"
2 changes: 1 addition & 1 deletion modules/gallvp/agat/spextractsequences/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,6 @@ name: "agat_spextractsequences"
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- bioconda::agat=1.4.0
2 changes: 1 addition & 1 deletion modules/gallvp/busco/busco/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@ name: busco_busco
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- bioconda::busco=5.7.1
2 changes: 1 addition & 1 deletion modules/gallvp/busco/busco/tests/main.nf.test
Original file line number Diff line number Diff line change
Expand Up @@ -126,7 +126,7 @@ nextflow_process {
}

assert snapshot(
process.out.batch_summary[0][1],
file(process.out.batch_summary[0][1]).name,
process.out.full_table[0][1],
process.out.missing_busco_list[0][1],
process.out.versions[0]
Expand Down
6 changes: 3 additions & 3 deletions modules/gallvp/busco/busco/tests/main.nf.test.snap
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@
},
"test_busco_genome_multi_fasta": {
"content": [
"test-bacteria_odb10-busco.batch_summary.txt:md5,fcd3c208913e8abda3d6742c43fec5fa",
"test-bacteria_odb10-busco.batch_summary.txt",
[
"full_table.tsv:md5,c657edcc7d0de0175869717551df6e83",
"full_table.tsv:md5,638fe7590f442c57361554dae330eca1"
Expand All @@ -159,9 +159,9 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.4"
},
"timestamp": "2024-05-03T13:23:50.255602"
"timestamp": "2024-08-22T11:24:24.828742"
},
"test_busco_eukaryote_metaeuk": {
"content": [
Expand Down
2 changes: 1 addition & 1 deletion modules/gallvp/busco/generateplot/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,6 @@ name: "busco_generateplot"
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- bioconda::busco=5.7.1
2 changes: 1 addition & 1 deletion modules/gallvp/custom/restoregffids/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,6 @@ name: "custom_restoregffids"
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- "python=3.10.2"
1 change: 0 additions & 1 deletion modules/gallvp/custom/shortenfastaids/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@ name: "custom_shortenfastaids"
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- biopython==1.75
Expand Down
2 changes: 1 addition & 1 deletion modules/gallvp/gffread/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@ name: gffread
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- bioconda::gffread=0.12.7
2 changes: 1 addition & 1 deletion modules/gallvp/ltrretriever/lai/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,6 @@ name: "ltrretriever_lai"
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- "bioconda::LTR_retriever=2.9.9"
2 changes: 1 addition & 1 deletion modules/gallvp/repeatmasker/repeatmasker/environment.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,6 @@ name: "repeatmasker_repeatmasker"
channels:
- conda-forge
- bioconda
- defaults

dependencies:
- "bioconda::repeatmasker=4.1.5"
5 changes: 4 additions & 1 deletion modules/nf-core/fastqc/main.nf

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