mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 23:43:08 +00:00
Fix final linting problems for template merge
This commit is contained in:
James A. Fellows Yates
parent
8fff741f85
commit
e64b3f85a4
2 changed files with 142 additions and 110 deletions
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@ -6,10 +6,9 @@ import sys
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import errno
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import errno
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import argparse
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import argparse
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def parse_args(args=None):
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def parse_args(args=None):
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Description = (
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Description = "Reformat nf-core/taxprofiler samplesheet file and check its contents."
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"Reformat nf-core/taxprofiler samplesheet file and check its contents."
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)
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Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
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Epilog = "Example usage: python check_samplesheet.py <FILE_IN> <FILE_OUT>"
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@ -18,6 +17,7 @@ def parse_args(args=None):
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parser.add_argument("FILE_OUT", help="Output file.")
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parser.add_argument("FILE_OUT", help="Output file.")
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return parser.parse_args(args)
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return parser.parse_args(args)
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def make_dir(path):
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def make_dir(path):
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if len(path) > 0:
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if len(path) > 0:
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try:
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try:
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@ -26,6 +26,7 @@ def make_dir(path):
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if exception.errno != errno.EEXIST:
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if exception.errno != errno.EEXIST:
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raise exception
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raise exception
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def print_error(error, context="Line", context_str=""):
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def print_error(error, context="Line", context_str=""):
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error_str = "ERROR: Please check samplesheet -> {}".format(error)
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error_str = "ERROR: Please check samplesheet -> {}".format(error)
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if context != "" and context_str != "":
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if context != "" and context_str != "":
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@ -35,6 +36,7 @@ def print_error(error, context="Line", context_str=""):
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print(error_str)
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print(error_str)
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sys.exit(1)
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sys.exit(1)
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def check_samplesheet(file_in, file_out):
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def check_samplesheet(file_in, file_out):
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"""
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"""
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This function checks that the samplesheet follows the following structure:
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This function checks that the samplesheet follows the following structure:
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@ -118,9 +120,7 @@ def check_samplesheet(file_in, file_out):
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num_cols = len([x for x in lspl if x])
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num_cols = len([x for x in lspl if x])
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if num_cols < MIN_COLS:
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if num_cols < MIN_COLS:
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print_error(
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print_error(
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"Invalid number of populated columns (minimum = {})!".format(
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"Invalid number of populated columns (minimum = {})!".format(MIN_COLS),
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MIN_COLS
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),
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"Line",
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"Line",
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line,
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line,
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)
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)
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@ -183,13 +183,9 @@ def check_samplesheet(file_in, file_out):
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## Auto-detect paired-end/single-end
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## Auto-detect paired-end/single-end
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if sample and fastq_1 and fastq_2: ## Paired-end short reads
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if sample and fastq_1 and fastq_2: ## Paired-end short reads
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sample_info.extend(["0", fastq_1, fastq_2, fasta])
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sample_info.extend(["0", fastq_1, fastq_2, fasta])
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elif (
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elif sample and fastq_1 and not fastq_2: ## Single-end short/long fastq reads
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sample and fastq_1 and not fastq_2
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): ## Single-end short/long fastq reads
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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elif (
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elif sample and fasta and not fastq_1 and not fastq_2: ## Single-end long reads
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sample and fasta and not fastq_1 and not fastq_2
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): ## Single-end long reads
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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sample_info.extend(["1", fastq_1, fastq_2, fasta])
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elif fasta and (fastq_1 or fastq_2):
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elif fasta and (fastq_1 or fastq_2):
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print_error(
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print_error(
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232
modules.json
232
modules.json
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@ -3,104 +3,140 @@
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"homePage": "https://github.com/nf-core/taxprofiler",
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"homePage": "https://github.com/nf-core/taxprofiler",
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"repos": {
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"repos": {
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"nf-core/modules": {
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"nf-core/modules": {
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"adapterremoval": {
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"git_url": "https://github.com/nf-core/modules.git",
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"git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
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"modules": {
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},
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"adapterremoval": {
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"bbmap/bbduk": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "879d42c5e28661fe0a5e744c9e2c515868f9e08a"
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},
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},
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"bowtie2/align": {
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"bbmap/bbduk": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"branch": "master",
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},
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"bowtie2/build": {
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},
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"bowtie2/align": {
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},
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"branch": "master",
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"cat/fastq": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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},
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"bowtie2/build": {
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"centrifuge/centrifuge": {
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"branch": "master",
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"git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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},
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"centrifuge/kreport": {
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"cat/fastq": {
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"git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
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"branch": "master",
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},
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"custom/dumpsoftwareversions": {
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},
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"centrifuge/centrifuge": {
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},
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"branch": "master",
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"diamond/blastx": {
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"git_sha": "d2726fcf75063960f06b36d2229a4c0966614108"
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"git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
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},
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},
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"centrifuge/kreport": {
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"fastp": {
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"branch": "master",
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"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
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"git_sha": "734d0db6079a4aa43b6509b207e5d6feb35d4838"
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},
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},
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"fastqc": {
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"custom/dumpsoftwareversions": {
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"branch": "master",
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},
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"filtlong": {
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},
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"git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
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"diamond/blastx": {
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},
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"branch": "master",
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"gunzip": {
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"git_sha": "3531824af826c16cd252bc5aa82ae169b244ebaa"
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"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
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},
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},
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"fastp": {
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"kaiju/kaiju": {
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"branch": "master",
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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"git_sha": "d0a1cbb703a130c19f6796c3fce24fbe7dfce789"
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},
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},
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"kaiju/kaiju2krona": {
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"fastqc": {
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"git_sha": "2f0b19240430de6807b1232e6d9d0e8084e8a28f"
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"branch": "master",
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},
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"kaiju/kaiju2table": {
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},
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"git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
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"filtlong": {
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},
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"branch": "master",
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"kraken2/kraken2": {
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"git_sha": "957cb9b83668075f4af101fc99502908cca487e3"
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"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
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},
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},
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"gunzip": {
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"krakentools/kreport2krona": {
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"branch": "master",
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"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
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"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
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},
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},
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"krona/ktimporttaxonomy": {
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"kaiju/kaiju": {
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"git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"
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"branch": "master",
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},
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"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
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"krona/ktimporttext": {
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},
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"git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
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"kaiju/kaiju2krona": {
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},
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"branch": "master",
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"malt/run": {
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"git_sha": "2f0b19240430de6807b1232e6d9d0e8084e8a28f"
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"git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"
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},
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},
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"kaiju/kaiju2table": {
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"megan/rma2info": {
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"branch": "master",
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"git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
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"git_sha": "538dbac98ba9c8f799536cd5a617195501439457"
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},
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},
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"metaphlan3": {
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"kraken2/kraken2": {
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"git_sha": "ed4dd1a928ebf4308efb720de878045f7773f8e2"
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"branch": "master",
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},
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"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
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"minimap2/align": {
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},
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"git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
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"krakentools/kreport2krona": {
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},
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"branch": "master",
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"minimap2/index": {
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"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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},
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"krona/ktimporttaxonomy": {
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"motus/merge": {
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"branch": "master",
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"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
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"git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"
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},
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},
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"motus/profile": {
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"krona/ktimporttext": {
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"git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
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"branch": "master",
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},
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"git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
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"multiqc": {
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},
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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"malt/run": {
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},
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"branch": "master",
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"porechop": {
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"git_sha": "be8d7b3293cac26cc63e4dbfb364deb8ed6ec7e5"
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"git_sha": "b78e19b9dae3671db2c7d4346fe04452c1debfab"
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},
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},
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"megan/rma2info": {
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"prinseqplusplus": {
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"branch": "master",
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"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
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"git_sha": "2d38566eca4cc15142b2ffa7c11837569b39aece"
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},
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},
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"samtools/bam2fq": {
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"metaphlan3": {
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"git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
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"branch": "master",
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},
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"git_sha": "ed4dd1a928ebf4308efb720de878045f7773f8e2"
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"samtools/view": {
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},
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"git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
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"minimap2/align": {
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},
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"branch": "master",
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"untar": {
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"git_sha": "1a5a9e7b4009dcf34e6867dd1a5a1d9a718b027b"
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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},
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"minimap2/index": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"motus/merge": {
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"branch": "master",
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"git_sha": "b02e648c221e1da17cb589eefe297e61ec9e9c49"
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},
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"motus/profile": {
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"branch": "master",
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"git_sha": "b6ed584443ad68ac41e6975994139454a4f23c18"
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
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},
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"porechop": {
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"branch": "master",
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"git_sha": "b78e19b9dae3671db2c7d4346fe04452c1debfab"
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},
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"prinseqplusplus": {
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"branch": "master",
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"git_sha": "f1c5384c31e985591716afdd732cf8c2ae29d05b"
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},
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"samtools/bam2fq": {
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"branch": "master",
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"git_sha": "5510ea39fe638594bc26ac34cadf4a84bf27d159"
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},
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"samtools/view": {
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"branch": "master",
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"git_sha": "6b64f9cb6c3dd3577931cc3cd032d6fb730000ce"
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},
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"untar": {
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"branch": "master",
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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}
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}
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}
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}
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}
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}
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}
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