Mercurial > repos > iuc > umi_tools_extract
annotate test-data/out_wl_paired.log @ 19:7a7e33d28f62 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
| author | iuc |
|---|---|
| date | Sat, 05 Oct 2024 13:07:19 +0000 |
| parents | 27ac32a22ad2 |
| children |
| rev | line source |
|---|---|
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15
27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
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changeset
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1 # UMI-tools version: 1.1.2 |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
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2 # output generated by whitelist --bc-pattern=CCCNNNNNNNNXXXXX --extract-method=string --subset-reads=0 --knee-method=density --stdin=input_read1.gz --read2-in=input_read2.gz --expect-cells=5 --error-correct-threshold=3 --method=reads --plot-prefix=OUT --log=/tmp/tmpcx2d26we/files/0/0/8/dataset_008b1843-bfa2-44fb-9d3c-52695bd9ce74.dat --log2stderr |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
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3 # job started at Tue Jul 13 15:21:12 2021 on MOLSYB009 -- ba3841c0-b2d5-4188-88ca-4ee241163293 |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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4 # pid: 1155608, system: Linux 5.4.0-74-generic #83-Ubuntu SMP Sat May 8 02:35:39 UTC 2021 x86_64 |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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5 # allow_threshold_error : False |
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3
475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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6 # blacklist_tsv : None |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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7 # cell_number : False |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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8 # compresslevel : 6 |
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15
27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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9 # ed_above_threshold : None |
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3
475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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10 # error_correct_threshold : 3 |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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11 # expect_cells : 5 |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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12 # extract_method : string |
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15
27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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13 # filtered_out : None |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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14 # filtered_out2 : None |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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15 # ignore_suffix : False |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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16 # knee_method : density |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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17 # log2stderr : True |
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3
475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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18 # loglevel : 1 |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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19 # method : reads |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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20 # pattern : CCCNNNNNNNNXXXXX |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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21 # pattern2 : None |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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22 # plot_prefix : OUT |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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23 # prime3 : None |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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24 # random_seed : None |
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15
27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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25 # read2_in : input_read2.gz |
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3
475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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26 # short_help : None |
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15
27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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27 # stderr : <_io.TextIOWrapper name='<stderr>' mode='w' encoding='utf-8'> |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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28 # stdin : <_io.TextIOWrapper name='input_read1.gz' encoding='ascii'> |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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29 # stdlog : <_io.TextIOWrapper name='/tmp/tmpcx2d26we/files/0/0/8/dataset_008b1843-bfa2-44fb-9d3c-52695bd9ce74.dat' mode='a' encoding='UTF-8'> |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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30 # stdout : <_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'> |
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3
475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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31 # subset_reads : 0 |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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32 # timeit_file : None |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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33 # timeit_header : None |
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475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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34 # timeit_name : all |
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15
27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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35 # tmpdir : None |
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3
475ee31c61d9
planemo upload commit 8da5246c32d60a49e6b6b9027c9adc0a31d4bc5a
iuc
parents:
diff
changeset
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36 # whitelist_tsv : None |
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15
27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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37 2021-07-13 15:21:12,587 INFO Starting barcode extraction |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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38 2021-07-13 15:21:12,588 INFO Parsed 0 reads |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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39 2021-07-13 15:21:12,590 INFO Starting - whitelist determination |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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40 2021-07-13 15:21:14,249 INFO Finished - whitelist determination |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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41 2021-07-13 15:21:14,249 INFO Starting - finding putative error cell barcodes |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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42 2021-07-13 15:21:14,249 INFO building bktree |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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43 2021-07-13 15:21:14,249 INFO done building bktree |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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44 2021-07-13 15:21:14,249 INFO Finished - finding putative error cell barcodes |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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45 2021-07-13 15:21:14,249 INFO Top 1 cell barcodes passed the selected threshold |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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46 2021-07-13 15:21:14,249 INFO Writing out whitelist |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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47 2021-07-13 15:21:14,249 INFO Parsed 100 reads |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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48 2021-07-13 15:21:14,249 INFO 100 reads matched the barcode pattern |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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49 2021-07-13 15:21:14,249 INFO Found 23 unique cell barcodes |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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50 2021-07-13 15:21:14,249 INFO Found 15 total reads matching the selected cell barcodes |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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51 2021-07-13 15:21:14,249 INFO Found 85 total reads which can be error corrected to the selected cell barcodes |
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27ac32a22ad2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents:
3
diff
changeset
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52 # job finished in 1 seconds at Tue Jul 13 15:21:14 2021 -- 7.19 0.62 0.08 0.02 -- ba3841c0-b2d5-4188-88ca-4ee241163293 |