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Finish Up Initial Docs and Fixing Linting
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# phac-nml/viralassembly: Example Commands | ||
A variety of example commands using different parameter options to display how to use each | ||
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## Amplicon | ||
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### Clair3 | ||
Clair3 with a local model, local scheme, fastq directory, conda, and the custom report output | ||
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```bash | ||
nextflow run phac-nml/viralassembly \ | ||
-profile conda \ | ||
--fastq_pass FASTQ_PASS/ \ | ||
--variant_caller 'clair3' \ | ||
--clair3_model ./r1041_e82_400bps_sup_v420 \ | ||
--local_scheme ./primer_schemes \ | ||
--scheme 'hCMV' \ | ||
--scheme_version 'V1' \ | ||
--custom_report \ | ||
--outdir ./results | ||
``` | ||
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### Medaka | ||
Minimal input medaka with conda, an input csv file for data, and the nCoV-2019 scheme | ||
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```bash | ||
nextflow run phac-nml/viralassembly \ | ||
-profile conda \ | ||
--input INPUT.csv \ | ||
--variant_caller 'medaka' \ | ||
--scheme 'nCoV-2019' \ | ||
--scheme_version 'V5.3.2' \ | ||
--outdir ./results | ||
``` | ||
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### Nanopolish | ||
Nanopolish run using singularity and the base artic command line tool (instead of the default nextflow implementation) | ||
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```bash | ||
nextflow run phac-nml/viralassembly \ | ||
-profile singularity \ | ||
--input INPUT.csv \ | ||
--fast5_pass FAST5_PASS/ \ | ||
--sequencing_summart SEQ_SUM.txt \ | ||
--variant_caller 'nanopolish' \ | ||
--scheme 'nCoV-2019' \ | ||
--scheme_version 'V5.3.2' \ | ||
--use_artic_tool \ | ||
--outdir ./results | ||
``` | ||
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-------------------------- | ||
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## Non-Amplicon | ||
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### Clair3 | ||
Minimal clair3 with docker using a fastq input directory along wth a gff3 reference file for SnpEff | ||
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```bash | ||
nextflow run phac-nml/viralassembly \ | ||
-profile docker \ | ||
--fastq_pass FASTQ_PASS/ \ | ||
--variant_caller 'clair3' \ | ||
--reference ./REFERENCE.fa \ | ||
--gff ./REFERENCE.gff | ||
``` | ||
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### Medaka | ||
Medaka with conda skipping QC and SnpEff | ||
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```bash | ||
nextflow run phac-nml/viralassembly \ | ||
-profile conda \ | ||
--input INPUT.csv \ | ||
--variant_caller 'medaka' \ | ||
--reference ./REFERENCE.fa \ | ||
--skip_qc \ | ||
--skip_snpeff | ||
``` | ||
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### Nanopolish | ||
Nanopolish running with conda, filtering the read lengths to be shorter, and creating a custom report | ||
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```bash | ||
nextflow run phac-nml/viralassembly \ | ||
-profile conda \ | ||
--input INPUT.csv \ | ||
--fast5_pass FAST5_PASS/ \ | ||
--sequencing_summart SEQ_SUM.txt \ | ||
--variant_caller 'nanopolish' \ | ||
--reference ./REFERENCE.fa \ | ||
--min_length 100 \ | ||
--max_length 600 \ | ||
--outdir ./results | ||
``` |
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docs/example_files/inputs/example_custom_scheme/virus/V1-custom/custom.reference.fasta
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>Custom.1 | ||
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT | ||
GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT | ||
CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC | ||
TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT | ||
CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC | ||
CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC | ||
TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT | ||
ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT |
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docs/example_files/inputs/example_custom_scheme/virus/V1-custom/custom.scheme.bed
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Custom.1 10 34 custom_1_LEFT 1 + | ||
Custom.1 300 320 custom_1_RIGHT 1 - | ||
Custom.1 220 246 custom_2_LEFT 2 + | ||
Custom.1 440 460 custom_2_RIGHT 2 - |
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sample,reads | ||
negative-ctrl-1,barcode11 | ||
run-ntc-1,barcode94 | ||
pos-ctrl-1,barcode95 | ||
cov-1,barcode5 | ||
cov-2,barcode01 | ||
cov-3,barcode12 | ||
cov-4,barcode19 | ||
cov-5,barcode40 | ||
cov-6,barcode61 | ||
cov-7,barcode75 |
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sample barcode run other | ||
negative-ctrl-1 11 example-run additional_info | ||
run-ntc-1 94 example-run additional_info | ||
pos-ctrl-1 95 example-run additional_info | ||
cov-1 5 example-run additional_info | ||
cov-2 1 example-run additional_info | ||
cov-3 12 example-run additional_info | ||
cov-4 19 example-run additional_info | ||
cov-5 40 example-run additional_info | ||
cov-6 61 example-run additional_info | ||
cov-7 75 example-run additional_info |
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