diff --git a/expected/README.md b/expected/README.md deleted file mode 100644 index 801bcfc..0000000 --- a/expected/README.md +++ /dev/null @@ -1,57 +0,0 @@ -# Expected results - - - -- [Structure](#structure) - - [Files of 1 byte](#files-of-1-byte) -- [How to verify results](#how-to-verify-results) - - [cgpwgs](#cgpwgs) -- [Why not a tar.gz file?](#why-not-a-targz-file) -- [maptime files](#maptime-files) - - - -## Structure - -This area reflects the structure of the examples tree. - -See [`examples/README.md`](../examples/README.md) for correlation to json param files. - -### Files of 1 byte - -We include all files in this area but those that are not considered useful for verification -purposes have been truncated to a size of 1 (newline char only). - -## How to verify results - -### cgpwgs - -The following files are to be used to compare results: - -* `*.bas` - Statistics of BAM/CRAM generated by `bam_stats`, tsv file. -* `*.met` - Statistics and histogram generated by `bammarkduplicates2`. - -A simple diff should be sufficient to verify. - -## Why not a tar.gz file? - -1. It's easier to see what files should be found in the result archive. -1. We truncate many of the files that don't aid in verification. - -## maptime files - -These are retained to allow us to look back over the runtimes for the test sets. Unfortunately -the tool generating these creates files that git doesn't like. - -When committing new versions of `*.maptime` files you will see the following error: - -``` -expected/....maptime:9: new blank line at EOF. -``` - -To correct these files a quick script is included so you can just run the following from the base -of the project: - -``` -find . -type file -iname \*.maptime -exec ./scripts/timeCleaner.pl {} \; -``` diff --git a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam b/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.bai b/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.bas b/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.bas deleted file mode 100644 index f768a18..0000000 --- a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.bas +++ /dev/null @@ -1,9 +0,0 @@ -bam_filename sample platform platform_unit library readgroup read_length_r1 read_length_r2 #_mapped_bases #_mapped_bases_r1 #_mapped_bases_r2 #_divergent_bases #_divergent_bases_r1 #_divergent_bases_r2 #_total_reads #_total_reads_r1 #_total_reads_r2 #_mapped_reads #_mapped_reads_r1 #_mapped_reads_r2 #_mapped_reads_properly_paired #_gc_bases_r1 #_gc_bases_r2 mean_insert_size insert_size_sd median_insert_size #_duplicate_reads #_mapped_pairs #_inter_chr_pairs #_qc_fail_r1 #_qc_fail_r2 -- test ILLUMINA 0_6 4471 10658 100 100 12497306 6248676 6248630 19 12 7 124974 62487 62487 124974 62487 62487 61211 2468179 2470818 299.847 24.277 300.000 10 62487 237 0 0 -- test ILLUMINA 0_8 4471 10659 100 100 12541938 6270984 6270954 18 13 5 125420 62710 62710 125420 62710 62710 62075 2474977 2472023 299.814 24.026 300.000 76 62710 93 0 0 -- test ILLUMINA 0_1 4471 10660 100 100 12451313 6225660 6225653 20 12 8 124514 62257 62257 124514 62257 62257 60972 2457268 2457738 299.904 23.798 299.000 104 62257 233 0 0 -- test ILLUMINA 0_4 4471 10661 100 100 12508135 6254069 6254066 27 12 15 125082 62541 62541 125082 62541 62541 61759 2473127 2467452 299.701 24.754 299.000 156 62541 112 0 0 -- test ILLUMINA 0_3 4471 10662 100 100 12508571 6254280 6254291 2 1 1 125086 62543 62543 125086 62543 62543 62423 2467579 2466872 299.553 26.702 300.000 234 62543 14 0 0 -- test ILLUMINA 0_7 4471 10663 100 100 12472347 6236178 6236169 5 1 4 124724 62362 62362 124724 62362 62362 62021 2462333 2459790 299.793 25.666 300.000 242 62362 53 0 0 -- test ILLUMINA 0_2 4471 10664 100 100 12526060 6263035 6263025 23 6 17 125262 62631 62631 125262 62631 62631 61805 2469221 2472495 300.821 24.790 300.000 276 62631 125 0 0 -- test ILLUMINA 0_5 4471 10665 100 100 12493677 6246853 6246824 12 4 8 124938 62469 62469 124938 62469 62469 61515 2465110 2468022 299.102 23.444 299.000 348 62469 160 0 0 diff --git a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.maptime b/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.maptime deleted file mode 100644 index f66c270..0000000 --- a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.maptime +++ /dev/null @@ -1,8 +0,0 @@ -command:bwa_mem.pl -o /var/spool/cwl -r /var/spool/cwl/reference_files/genome.fa -s test -f 1000000 -t 28 -mt 28 -l /usr/lib/libtcmalloc_minimal.so -b -Y -K 100000000 /var/lib/cwl/stgf656c48f-4d47-4882-afc5-3aedd8406397/insilico_21.bam -real:132.64 -user:289.64 -sys:36.62 -pctCpu:245% -text:0k -data:0k -max:5529676k diff --git a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.md5 b/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.md5 deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.md5 +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.met b/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.met deleted file mode 100644 index fa9aa10..0000000 --- a/expected/cgpmap/bamBaiOut/bam_in/bam_in.bam.met +++ /dev/null @@ -1,108 +0,0 @@ -# /opt/wtsi-cgp/biobambam2/bin/bammarkduplicates2 tmpfile=/var/spool/cwl/tmpMap_test/biormdup level=0 markthreads=27 M=/var/spool/cwl/test.bam.met - -##METRICS -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -4471 0 500000 0 0 723 0 0.001446 172724026 - -## HISTOGRAM -BIN VALUE -1 1 -2 1.99711 -3 2.99134 -4 3.98269 -5 4.97118 -6 5.95681 -7 6.93959 -8 7.91953 -9 8.89664 -10 9.87092 -11 10.8424 -12 11.811 -13 12.7769 -14 13.74 -15 14.7003 -16 15.6578 -17 16.6125 -18 17.5645 -19 18.5137 -20 19.4602 -21 20.4039 -22 21.345 -23 22.2833 -24 23.2189 -25 24.1517 -26 25.0819 -27 26.0094 -28 26.9342 -29 27.8564 -30 28.7759 -31 29.6927 -32 30.6068 -33 31.5184 -34 32.4273 -35 33.3335 -36 34.2372 -37 35.1382 -38 36.0366 -39 36.9325 -40 37.8257 -41 38.7164 -42 39.6045 -43 40.49 -44 41.3729 -45 42.2534 -46 43.1312 -47 44.0065 -48 44.8793 -49 45.7496 -50 46.6174 -51 47.4826 -52 48.3454 -53 49.2056 -54 50.0634 -55 50.9187 -56 51.7715 -57 52.6218 -58 53.4697 -59 54.3152 -60 55.1582 -61 55.9987 -62 56.8368 -63 57.6725 -64 58.5058 -65 59.3367 -66 60.1652 -67 60.9913 -68 61.815 -69 62.6363 -70 63.4552 -71 64.2718 -72 65.086 -73 65.8979 -74 66.7074 -75 67.5146 -76 68.3194 -77 69.1219 -78 69.9221 -79 70.72 -80 71.5156 -81 72.3089 -82 73.0999 -83 73.8886 -84 74.675 -85 75.4591 -86 76.241 -87 77.0206 -88 77.798 -89 78.5731 -90 79.346 -91 80.1166 -92 80.885 -93 81.6512 -94 82.4152 -95 83.177 -96 83.9365 -97 84.6939 -98 85.4491 -99 86.2021 -100 86.9529 diff --git a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam b/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.bai b/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.bas b/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.bas deleted file mode 100644 index f768a18..0000000 --- a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.bas +++ /dev/null @@ -1,9 +0,0 @@ -bam_filename sample platform platform_unit library readgroup read_length_r1 read_length_r2 #_mapped_bases #_mapped_bases_r1 #_mapped_bases_r2 #_divergent_bases #_divergent_bases_r1 #_divergent_bases_r2 #_total_reads #_total_reads_r1 #_total_reads_r2 #_mapped_reads #_mapped_reads_r1 #_mapped_reads_r2 #_mapped_reads_properly_paired #_gc_bases_r1 #_gc_bases_r2 mean_insert_size insert_size_sd median_insert_size #_duplicate_reads #_mapped_pairs #_inter_chr_pairs #_qc_fail_r1 #_qc_fail_r2 -- test ILLUMINA 0_6 4471 10658 100 100 12497306 6248676 6248630 19 12 7 124974 62487 62487 124974 62487 62487 61211 2468179 2470818 299.847 24.277 300.000 10 62487 237 0 0 -- test ILLUMINA 0_8 4471 10659 100 100 12541938 6270984 6270954 18 13 5 125420 62710 62710 125420 62710 62710 62075 2474977 2472023 299.814 24.026 300.000 76 62710 93 0 0 -- test ILLUMINA 0_1 4471 10660 100 100 12451313 6225660 6225653 20 12 8 124514 62257 62257 124514 62257 62257 60972 2457268 2457738 299.904 23.798 299.000 104 62257 233 0 0 -- test ILLUMINA 0_4 4471 10661 100 100 12508135 6254069 6254066 27 12 15 125082 62541 62541 125082 62541 62541 61759 2473127 2467452 299.701 24.754 299.000 156 62541 112 0 0 -- test ILLUMINA 0_3 4471 10662 100 100 12508571 6254280 6254291 2 1 1 125086 62543 62543 125086 62543 62543 62423 2467579 2466872 299.553 26.702 300.000 234 62543 14 0 0 -- test ILLUMINA 0_7 4471 10663 100 100 12472347 6236178 6236169 5 1 4 124724 62362 62362 124724 62362 62362 62021 2462333 2459790 299.793 25.666 300.000 242 62362 53 0 0 -- test ILLUMINA 0_2 4471 10664 100 100 12526060 6263035 6263025 23 6 17 125262 62631 62631 125262 62631 62631 61805 2469221 2472495 300.821 24.790 300.000 276 62631 125 0 0 -- test ILLUMINA 0_5 4471 10665 100 100 12493677 6246853 6246824 12 4 8 124938 62469 62469 124938 62469 62469 61515 2465110 2468022 299.102 23.444 299.000 348 62469 160 0 0 diff --git a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.maptime b/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.maptime deleted file mode 100644 index affd73a..0000000 --- a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.maptime +++ /dev/null @@ -1,8 +0,0 @@ -command:bwa_mem.pl -o /var/spool/cwl -r /var/spool/cwl/reference_files/genome.fa -s test -f 1000000 -t 28 -mt 28 -l /usr/lib/libtcmalloc_minimal.so -b -Y -K 100000000 /var/lib/cwl/stgc3867845-4e8a-45ce-b4b7-528db5bdf08a/insilico_21.cram -real:131.11 -user:285.10 -sys:35.66 -pctCpu:244% -text:0k -data:0k -max:5521800k diff --git a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.md5 b/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.md5 deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.md5 +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.met b/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.met deleted file mode 100644 index fa9aa10..0000000 --- a/expected/cgpmap/bamBaiOut/cram_in/cram_in.bam.met +++ /dev/null @@ -1,108 +0,0 @@ -# /opt/wtsi-cgp/biobambam2/bin/bammarkduplicates2 tmpfile=/var/spool/cwl/tmpMap_test/biormdup level=0 markthreads=27 M=/var/spool/cwl/test.bam.met - -##METRICS -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -4471 0 500000 0 0 723 0 0.001446 172724026 - -## HISTOGRAM -BIN VALUE -1 1 -2 1.99711 -3 2.99134 -4 3.98269 -5 4.97118 -6 5.95681 -7 6.93959 -8 7.91953 -9 8.89664 -10 9.87092 -11 10.8424 -12 11.811 -13 12.7769 -14 13.74 -15 14.7003 -16 15.6578 -17 16.6125 -18 17.5645 -19 18.5137 -20 19.4602 -21 20.4039 -22 21.345 -23 22.2833 -24 23.2189 -25 24.1517 -26 25.0819 -27 26.0094 -28 26.9342 -29 27.8564 -30 28.7759 -31 29.6927 -32 30.6068 -33 31.5184 -34 32.4273 -35 33.3335 -36 34.2372 -37 35.1382 -38 36.0366 -39 36.9325 -40 37.8257 -41 38.7164 -42 39.6045 -43 40.49 -44 41.3729 -45 42.2534 -46 43.1312 -47 44.0065 -48 44.8793 -49 45.7496 -50 46.6174 -51 47.4826 -52 48.3454 -53 49.2056 -54 50.0634 -55 50.9187 -56 51.7715 -57 52.6218 -58 53.4697 -59 54.3152 -60 55.1582 -61 55.9987 -62 56.8368 -63 57.6725 -64 58.5058 -65 59.3367 -66 60.1652 -67 60.9913 -68 61.815 -69 62.6363 -70 63.4552 -71 64.2718 -72 65.086 -73 65.8979 -74 66.7074 -75 67.5146 -76 68.3194 -77 69.1219 -78 69.9221 -79 70.72 -80 71.5156 -81 72.3089 -82 73.0999 -83 73.8886 -84 74.675 -85 75.4591 -86 76.241 -87 77.0206 -88 77.798 -89 78.5731 -90 79.346 -91 80.1166 -92 80.885 -93 81.6512 -94 82.4152 -95 83.177 -96 83.9365 -97 84.6939 -98 85.4491 -99 86.2021 -100 86.9529 diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam b/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.bai b/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.bas b/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.bas deleted file mode 100644 index f768a18..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.bas +++ /dev/null @@ -1,9 +0,0 @@ -bam_filename sample platform platform_unit library readgroup read_length_r1 read_length_r2 #_mapped_bases #_mapped_bases_r1 #_mapped_bases_r2 #_divergent_bases #_divergent_bases_r1 #_divergent_bases_r2 #_total_reads #_total_reads_r1 #_total_reads_r2 #_mapped_reads #_mapped_reads_r1 #_mapped_reads_r2 #_mapped_reads_properly_paired #_gc_bases_r1 #_gc_bases_r2 mean_insert_size insert_size_sd median_insert_size #_duplicate_reads #_mapped_pairs #_inter_chr_pairs #_qc_fail_r1 #_qc_fail_r2 -- test ILLUMINA 0_6 4471 10658 100 100 12497306 6248676 6248630 19 12 7 124974 62487 62487 124974 62487 62487 61211 2468179 2470818 299.847 24.277 300.000 10 62487 237 0 0 -- test ILLUMINA 0_8 4471 10659 100 100 12541938 6270984 6270954 18 13 5 125420 62710 62710 125420 62710 62710 62075 2474977 2472023 299.814 24.026 300.000 76 62710 93 0 0 -- test ILLUMINA 0_1 4471 10660 100 100 12451313 6225660 6225653 20 12 8 124514 62257 62257 124514 62257 62257 60972 2457268 2457738 299.904 23.798 299.000 104 62257 233 0 0 -- test ILLUMINA 0_4 4471 10661 100 100 12508135 6254069 6254066 27 12 15 125082 62541 62541 125082 62541 62541 61759 2473127 2467452 299.701 24.754 299.000 156 62541 112 0 0 -- test ILLUMINA 0_3 4471 10662 100 100 12508571 6254280 6254291 2 1 1 125086 62543 62543 125086 62543 62543 62423 2467579 2466872 299.553 26.702 300.000 234 62543 14 0 0 -- test ILLUMINA 0_7 4471 10663 100 100 12472347 6236178 6236169 5 1 4 124724 62362 62362 124724 62362 62362 62021 2462333 2459790 299.793 25.666 300.000 242 62362 53 0 0 -- test ILLUMINA 0_2 4471 10664 100 100 12526060 6263035 6263025 23 6 17 125262 62631 62631 125262 62631 62631 61805 2469221 2472495 300.821 24.790 300.000 276 62631 125 0 0 -- test ILLUMINA 0_5 4471 10665 100 100 12493677 6246853 6246824 12 4 8 124938 62469 62469 124938 62469 62469 61515 2465110 2468022 299.102 23.444 299.000 348 62469 160 0 0 diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.maptime b/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.maptime deleted file mode 100644 index 1a065d3..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.maptime +++ /dev/null @@ -1,8 +0,0 @@ -command:bwa_mem.pl -o /var/spool/cwl -r /var/spool/cwl/reference_files/genome.fa -s test -f 1000000 -t 28 -mt 28 -l /usr/lib/libtcmalloc_minimal.so -b -Y -K 100000000 -g /var/lib/cwl/stg32389f61-6514-41c3-b5b7-be3a394b9689/insilico_21_fq.yaml /var/lib/cwl/stge2ffa3fa-5fc0-4966-bbf2-6c8a7ae7fc27/insilico_21_10658_i.fq.gz /var/lib/cwl/stg8d7a8397-974f-4daf-ae89-dc5ee88c157b/insilico_21_10659_i.fq.gz /var/lib/cwl/stgfc93a6c0-5182-4a09-a3c2-e561c74d292f/insilico_21_10660_i.fq.gz /var/lib/cwl/stgb20a8355-27ff-4fc1-926f-aff872c679d3/insilico_21_10661_i.fq.gz /var/lib/cwl/stg5901eaf5-328c-43e7-b403-750ef5631819/insilico_21_10662_i.fq.gz /var/lib/cwl/stg84355f83-c89c-465d-8245-d8cacb53bf93/insilico_21_10663_i.fq.gz /var/lib/cwl/stg6ae6f903-d039-4284-bc3b-a4d7787bbcd0/insilico_21_10664_i.fq.gz /var/lib/cwl/stgc130cbc7-e8cf-4b71-8e06-27e35cce83ab/insilico_21_10665_i.fq.gz -real:164.73 -user:285.27 -sys:37.13 -pctCpu:195% -text:0k -data:0k -max:5530000k diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.md5 b/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.md5 deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.md5 +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.met b/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.met deleted file mode 100644 index fa9aa10..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in/fq_gz_in.bam.met +++ /dev/null @@ -1,108 +0,0 @@ -# /opt/wtsi-cgp/biobambam2/bin/bammarkduplicates2 tmpfile=/var/spool/cwl/tmpMap_test/biormdup level=0 markthreads=27 M=/var/spool/cwl/test.bam.met - -##METRICS -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -4471 0 500000 0 0 723 0 0.001446 172724026 - -## HISTOGRAM -BIN VALUE -1 1 -2 1.99711 -3 2.99134 -4 3.98269 -5 4.97118 -6 5.95681 -7 6.93959 -8 7.91953 -9 8.89664 -10 9.87092 -11 10.8424 -12 11.811 -13 12.7769 -14 13.74 -15 14.7003 -16 15.6578 -17 16.6125 -18 17.5645 -19 18.5137 -20 19.4602 -21 20.4039 -22 21.345 -23 22.2833 -24 23.2189 -25 24.1517 -26 25.0819 -27 26.0094 -28 26.9342 -29 27.8564 -30 28.7759 -31 29.6927 -32 30.6068 -33 31.5184 -34 32.4273 -35 33.3335 -36 34.2372 -37 35.1382 -38 36.0366 -39 36.9325 -40 37.8257 -41 38.7164 -42 39.6045 -43 40.49 -44 41.3729 -45 42.2534 -46 43.1312 -47 44.0065 -48 44.8793 -49 45.7496 -50 46.6174 -51 47.4826 -52 48.3454 -53 49.2056 -54 50.0634 -55 50.9187 -56 51.7715 -57 52.6218 -58 53.4697 -59 54.3152 -60 55.1582 -61 55.9987 -62 56.8368 -63 57.6725 -64 58.5058 -65 59.3367 -66 60.1652 -67 60.9913 -68 61.815 -69 62.6363 -70 63.4552 -71 64.2718 -72 65.086 -73 65.8979 -74 66.7074 -75 67.5146 -76 68.3194 -77 69.1219 -78 69.9221 -79 70.72 -80 71.5156 -81 72.3089 -82 73.0999 -83 73.8886 -84 74.675 -85 75.4591 -86 76.241 -87 77.0206 -88 77.798 -89 78.5731 -90 79.346 -91 80.1166 -92 80.885 -93 81.6512 -94 82.4152 -95 83.177 -96 83.9365 -97 84.6939 -98 85.4491 -99 86.2021 -100 86.9529 diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam b/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.bai b/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.bas b/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.bas deleted file mode 100644 index f768a18..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.bas +++ /dev/null @@ -1,9 +0,0 @@ -bam_filename sample platform platform_unit library readgroup read_length_r1 read_length_r2 #_mapped_bases #_mapped_bases_r1 #_mapped_bases_r2 #_divergent_bases #_divergent_bases_r1 #_divergent_bases_r2 #_total_reads #_total_reads_r1 #_total_reads_r2 #_mapped_reads #_mapped_reads_r1 #_mapped_reads_r2 #_mapped_reads_properly_paired #_gc_bases_r1 #_gc_bases_r2 mean_insert_size insert_size_sd median_insert_size #_duplicate_reads #_mapped_pairs #_inter_chr_pairs #_qc_fail_r1 #_qc_fail_r2 -- test ILLUMINA 0_6 4471 10658 100 100 12497306 6248676 6248630 19 12 7 124974 62487 62487 124974 62487 62487 61211 2468179 2470818 299.847 24.277 300.000 10 62487 237 0 0 -- test ILLUMINA 0_8 4471 10659 100 100 12541938 6270984 6270954 18 13 5 125420 62710 62710 125420 62710 62710 62075 2474977 2472023 299.814 24.026 300.000 76 62710 93 0 0 -- test ILLUMINA 0_1 4471 10660 100 100 12451313 6225660 6225653 20 12 8 124514 62257 62257 124514 62257 62257 60972 2457268 2457738 299.904 23.798 299.000 104 62257 233 0 0 -- test ILLUMINA 0_4 4471 10661 100 100 12508135 6254069 6254066 27 12 15 125082 62541 62541 125082 62541 62541 61759 2473127 2467452 299.701 24.754 299.000 156 62541 112 0 0 -- test ILLUMINA 0_3 4471 10662 100 100 12508571 6254280 6254291 2 1 1 125086 62543 62543 125086 62543 62543 62423 2467579 2466872 299.553 26.702 300.000 234 62543 14 0 0 -- test ILLUMINA 0_7 4471 10663 100 100 12472347 6236178 6236169 5 1 4 124724 62362 62362 124724 62362 62362 62021 2462333 2459790 299.793 25.666 300.000 242 62362 53 0 0 -- test ILLUMINA 0_2 4471 10664 100 100 12526060 6263035 6263025 23 6 17 125262 62631 62631 125262 62631 62631 61805 2469221 2472495 300.821 24.790 300.000 276 62631 125 0 0 -- test ILLUMINA 0_5 4471 10665 100 100 12493677 6246853 6246824 12 4 8 124938 62469 62469 124938 62469 62469 61515 2465110 2468022 299.102 23.444 299.000 348 62469 160 0 0 diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.maptime b/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.maptime deleted file mode 100644 index 30c3ed5..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.maptime +++ /dev/null @@ -1,8 +0,0 @@ -command:bwa_mem.pl -o /var/spool/cwl -r /var/spool/cwl/reference_files/genome.fa -s test -f 1000000 -t 28 -mt 28 -l /usr/lib/libtcmalloc_minimal.so -b -Y -K 100000000 -g /var/lib/cwl/stg5276e019-e4e5-4e4c-bf84-dc20cb6c646c/insilico_21_fq.yaml --mmqc --mmqcfrac 0.05 /var/lib/cwl/stg36f91a9a-cceb-4f36-8f57-cc4739377d6f/insilico_21_10658_i.fq.gz /var/lib/cwl/stgecbec1c3-13d9-4230-a579-43235835d817/insilico_21_10659_i.fq.gz /var/lib/cwl/stg9b8c7798-c50f-41a9-930f-ffd3bbde47fc/insilico_21_10660_i.fq.gz /var/lib/cwl/stga3b817cb-0546-47c2-aa2c-244fc6dda2ac/insilico_21_10661_i.fq.gz /var/lib/cwl/stga7251f76-52df-4395-8835-bfe7dc9fe4b2/insilico_21_10662_i.fq.gz /var/lib/cwl/stg1d847bcd-77e8-47c6-99f9-413dbcbc7dcb/insilico_21_10663_i.fq.gz /var/lib/cwl/stg9d786b2f-e3dd-40fe-8d79-f33f80c6d7fb/insilico_21_10664_i.fq.gz /var/lib/cwl/stgd1a2a690-73ce-4857-a763-1504a036b502/insilico_21_10665_i.fq.gz -real:168.10 -user:287.27 -sys:39.02 -pctCpu:194% -text:0k -data:0k -max:5530808k diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.md5 b/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.md5 deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.md5 +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.met b/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.met deleted file mode 100644 index fa9aa10..0000000 --- a/expected/cgpmap/bamBaiOut/fq_gz_in_qcreads/fq_gz_in_qcreads.bam.met +++ /dev/null @@ -1,108 +0,0 @@ -# /opt/wtsi-cgp/biobambam2/bin/bammarkduplicates2 tmpfile=/var/spool/cwl/tmpMap_test/biormdup level=0 markthreads=27 M=/var/spool/cwl/test.bam.met - -##METRICS -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -4471 0 500000 0 0 723 0 0.001446 172724026 - -## HISTOGRAM -BIN VALUE -1 1 -2 1.99711 -3 2.99134 -4 3.98269 -5 4.97118 -6 5.95681 -7 6.93959 -8 7.91953 -9 8.89664 -10 9.87092 -11 10.8424 -12 11.811 -13 12.7769 -14 13.74 -15 14.7003 -16 15.6578 -17 16.6125 -18 17.5645 -19 18.5137 -20 19.4602 -21 20.4039 -22 21.345 -23 22.2833 -24 23.2189 -25 24.1517 -26 25.0819 -27 26.0094 -28 26.9342 -29 27.8564 -30 28.7759 -31 29.6927 -32 30.6068 -33 31.5184 -34 32.4273 -35 33.3335 -36 34.2372 -37 35.1382 -38 36.0366 -39 36.9325 -40 37.8257 -41 38.7164 -42 39.6045 -43 40.49 -44 41.3729 -45 42.2534 -46 43.1312 -47 44.0065 -48 44.8793 -49 45.7496 -50 46.6174 -51 47.4826 -52 48.3454 -53 49.2056 -54 50.0634 -55 50.9187 -56 51.7715 -57 52.6218 -58 53.4697 -59 54.3152 -60 55.1582 -61 55.9987 -62 56.8368 -63 57.6725 -64 58.5058 -65 59.3367 -66 60.1652 -67 60.9913 -68 61.815 -69 62.6363 -70 63.4552 -71 64.2718 -72 65.086 -73 65.8979 -74 66.7074 -75 67.5146 -76 68.3194 -77 69.1219 -78 69.9221 -79 70.72 -80 71.5156 -81 72.3089 -82 73.0999 -83 73.8886 -84 74.675 -85 75.4591 -86 76.241 -87 77.0206 -88 77.798 -89 78.5731 -90 79.346 -91 80.1166 -92 80.885 -93 81.6512 -94 82.4152 -95 83.177 -96 83.9365 -97 84.6939 -98 85.4491 -99 86.2021 -100 86.9529 diff --git a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam b/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.bai b/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.bai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.bai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.bas b/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.bas deleted file mode 100644 index f768a18..0000000 --- a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.bas +++ /dev/null @@ -1,9 +0,0 @@ -bam_filename sample platform platform_unit library readgroup read_length_r1 read_length_r2 #_mapped_bases #_mapped_bases_r1 #_mapped_bases_r2 #_divergent_bases #_divergent_bases_r1 #_divergent_bases_r2 #_total_reads #_total_reads_r1 #_total_reads_r2 #_mapped_reads #_mapped_reads_r1 #_mapped_reads_r2 #_mapped_reads_properly_paired #_gc_bases_r1 #_gc_bases_r2 mean_insert_size insert_size_sd median_insert_size #_duplicate_reads #_mapped_pairs #_inter_chr_pairs #_qc_fail_r1 #_qc_fail_r2 -- test ILLUMINA 0_6 4471 10658 100 100 12497306 6248676 6248630 19 12 7 124974 62487 62487 124974 62487 62487 61211 2468179 2470818 299.847 24.277 300.000 10 62487 237 0 0 -- test ILLUMINA 0_8 4471 10659 100 100 12541938 6270984 6270954 18 13 5 125420 62710 62710 125420 62710 62710 62075 2474977 2472023 299.814 24.026 300.000 76 62710 93 0 0 -- test ILLUMINA 0_1 4471 10660 100 100 12451313 6225660 6225653 20 12 8 124514 62257 62257 124514 62257 62257 60972 2457268 2457738 299.904 23.798 299.000 104 62257 233 0 0 -- test ILLUMINA 0_4 4471 10661 100 100 12508135 6254069 6254066 27 12 15 125082 62541 62541 125082 62541 62541 61759 2473127 2467452 299.701 24.754 299.000 156 62541 112 0 0 -- test ILLUMINA 0_3 4471 10662 100 100 12508571 6254280 6254291 2 1 1 125086 62543 62543 125086 62543 62543 62423 2467579 2466872 299.553 26.702 300.000 234 62543 14 0 0 -- test ILLUMINA 0_7 4471 10663 100 100 12472347 6236178 6236169 5 1 4 124724 62362 62362 124724 62362 62362 62021 2462333 2459790 299.793 25.666 300.000 242 62362 53 0 0 -- test ILLUMINA 0_2 4471 10664 100 100 12526060 6263035 6263025 23 6 17 125262 62631 62631 125262 62631 62631 61805 2469221 2472495 300.821 24.790 300.000 276 62631 125 0 0 -- test ILLUMINA 0_5 4471 10665 100 100 12493677 6246853 6246824 12 4 8 124938 62469 62469 124938 62469 62469 61515 2465110 2468022 299.102 23.444 299.000 348 62469 160 0 0 diff --git a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.csi b/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.csi deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.csi +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.maptime b/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.maptime deleted file mode 100644 index 744a695..0000000 --- a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.maptime +++ /dev/null @@ -1,8 +0,0 @@ -command:bwa_mem.pl -o /var/spool/cwl -r /var/spool/cwl/reference_files/genome.fa -s test -f 1000000 -t 28 -mt 28 -l /usr/lib/libtcmalloc_minimal.so -b -Y -K 100000000 -g /var/lib/cwl/stg21c46345-0fa4-44e7-8703-eceaefe6c6cb/insilico_21_fq.yaml --csi /var/lib/cwl/stgb8141f51-6ac0-4b91-95a8-60e2f9f969ff/insilico_21_10658_i.fq.gz /var/lib/cwl/stg3af22cae-2032-4225-b890-9627fd5b9cc3/insilico_21_10659_i.fq.gz /var/lib/cwl/stgf250b3a8-2d9c-4367-8641-b7ece78641d6/insilico_21_10660_i.fq.gz /var/lib/cwl/stg8d52a216-653c-47a9-85c4-bd588982d46f/insilico_21_10661_i.fq.gz /var/lib/cwl/stg0be3752e-4bbe-4c1f-b3ff-865649ae80a0/insilico_21_10662_i.fq.gz /var/lib/cwl/stg34794436-69af-42d6-a25d-64e25bf686c8/insilico_21_10663_i.fq.gz /var/lib/cwl/stgaf6054a1-f0db-4c43-a884-503690668a3a/insilico_21_10664_i.fq.gz /var/lib/cwl/stg991dff5b-cc7f-4e40-9e9c-c131dc57d4a1/insilico_21_10665_i.fq.gz -real:164.60 -user:280.00 -sys:36.66 -pctCpu:192% -text:0k -data:0k -max:5528892k diff --git a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.md5 b/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.md5 deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.md5 +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.met b/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.met deleted file mode 100644 index fa9aa10..0000000 --- a/expected/cgpmap/bamCsiOut/fq_gz_in/fq_gz_in.bam.met +++ /dev/null @@ -1,108 +0,0 @@ -# /opt/wtsi-cgp/biobambam2/bin/bammarkduplicates2 tmpfile=/var/spool/cwl/tmpMap_test/biormdup level=0 markthreads=27 M=/var/spool/cwl/test.bam.met - -##METRICS -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -4471 0 500000 0 0 723 0 0.001446 172724026 - -## HISTOGRAM -BIN VALUE -1 1 -2 1.99711 -3 2.99134 -4 3.98269 -5 4.97118 -6 5.95681 -7 6.93959 -8 7.91953 -9 8.89664 -10 9.87092 -11 10.8424 -12 11.811 -13 12.7769 -14 13.74 -15 14.7003 -16 15.6578 -17 16.6125 -18 17.5645 -19 18.5137 -20 19.4602 -21 20.4039 -22 21.345 -23 22.2833 -24 23.2189 -25 24.1517 -26 25.0819 -27 26.0094 -28 26.9342 -29 27.8564 -30 28.7759 -31 29.6927 -32 30.6068 -33 31.5184 -34 32.4273 -35 33.3335 -36 34.2372 -37 35.1382 -38 36.0366 -39 36.9325 -40 37.8257 -41 38.7164 -42 39.6045 -43 40.49 -44 41.3729 -45 42.2534 -46 43.1312 -47 44.0065 -48 44.8793 -49 45.7496 -50 46.6174 -51 47.4826 -52 48.3454 -53 49.2056 -54 50.0634 -55 50.9187 -56 51.7715 -57 52.6218 -58 53.4697 -59 54.3152 -60 55.1582 -61 55.9987 -62 56.8368 -63 57.6725 -64 58.5058 -65 59.3367 -66 60.1652 -67 60.9913 -68 61.815 -69 62.6363 -70 63.4552 -71 64.2718 -72 65.086 -73 65.8979 -74 66.7074 -75 67.5146 -76 68.3194 -77 69.1219 -78 69.9221 -79 70.72 -80 71.5156 -81 72.3089 -82 73.0999 -83 73.8886 -84 74.675 -85 75.4591 -86 76.241 -87 77.0206 -88 77.798 -89 78.5731 -90 79.346 -91 80.1166 -92 80.885 -93 81.6512 -94 82.4152 -95 83.177 -96 83.9365 -97 84.6939 -98 85.4491 -99 86.2021 -100 86.9529 diff --git a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram b/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.bas b/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.bas deleted file mode 100644 index 3f11bd9..0000000 --- a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.bas +++ /dev/null @@ -1,9 +0,0 @@ -bam_filename sample platform platform_unit library readgroup read_length_r1 read_length_r2 #_mapped_bases #_mapped_bases_r1 #_mapped_bases_r2 #_divergent_bases #_divergent_bases_r1 #_divergent_bases_r2 #_total_reads #_total_reads_r1 #_total_reads_r2 #_mapped_reads #_mapped_reads_r1 #_mapped_reads_r2 #_mapped_reads_properly_paired #_gc_bases_r1 #_gc_bases_r2 mean_insert_size insert_size_sd median_insert_size #_duplicate_reads #_mapped_pairs #_inter_chr_pairs #_qc_fail_r1 #_qc_fail_r2 -test.cram test ILLUMINA 0_6 4471 10658 100 100 12497306 6248676 6248630 19 12 7 124974 62487 62487 124974 62487 62487 61211 2468179 2470818 299.847 24.277 300.000 10 62487 237 0 0 -test.cram test ILLUMINA 0_8 4471 10659 100 100 12541938 6270984 6270954 18 13 5 125420 62710 62710 125420 62710 62710 62075 2474977 2472023 299.814 24.026 300.000 76 62710 93 0 0 -test.cram test ILLUMINA 0_1 4471 10660 100 100 12451313 6225660 6225653 20 12 8 124514 62257 62257 124514 62257 62257 60972 2457268 2457738 299.904 23.798 299.000 104 62257 233 0 0 -test.cram test ILLUMINA 0_4 4471 10661 100 100 12508135 6254069 6254066 27 12 15 125082 62541 62541 125082 62541 62541 61759 2473127 2467452 299.701 24.754 299.000 156 62541 112 0 0 -test.cram test ILLUMINA 0_3 4471 10662 100 100 12508571 6254280 6254291 2 1 1 125086 62543 62543 125086 62543 62543 62423 2467579 2466872 299.553 26.702 300.000 234 62543 14 0 0 -test.cram test ILLUMINA 0_7 4471 10663 100 100 12472347 6236178 6236169 5 1 4 124724 62362 62362 124724 62362 62362 62021 2462333 2459790 299.793 25.666 300.000 242 62362 53 0 0 -test.cram test ILLUMINA 0_2 4471 10664 100 100 12526060 6263035 6263025 23 6 17 125262 62631 62631 125262 62631 62631 61805 2469221 2472495 300.821 24.790 300.000 276 62631 125 0 0 -test.cram test ILLUMINA 0_5 4471 10665 100 100 12493677 6246853 6246824 12 4 8 124938 62469 62469 124938 62469 62469 61515 2465110 2468022 299.102 23.444 299.000 348 62469 160 0 0 diff --git a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.crai b/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.crai deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.crai +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.maptime b/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.maptime deleted file mode 100644 index f0068d1..0000000 --- a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.maptime +++ /dev/null @@ -1,8 +0,0 @@ -command:bwa_mem.pl -o /var/spool/cwl -r /var/spool/cwl/reference_files/genome.fa -s test -f 1000000 -t 28 -mt 28 -c -l /usr/lib/libtcmalloc_minimal.so -b -Y -K 100000000 -g /var/lib/cwl/stg539e032a-403f-4317-8f40-cbe2c8b44b64/insilico_21_fq.yaml /var/lib/cwl/stgbcac115c-7427-47f0-9379-9a9b1514fd47/insilico_21_10658_i.fq.gz /var/lib/cwl/stg509fbc83-2a0e-4700-a441-d925602363df/insilico_21_10659_i.fq.gz /var/lib/cwl/stgb45da067-d3bd-496c-bac7-de54569ad3da/insilico_21_10660_i.fq.gz /var/lib/cwl/stg1199032d-b77e-4e83-a06d-ec469be3c0af/insilico_21_10661_i.fq.gz /var/lib/cwl/stg819f6f16-b4eb-4060-b7f8-833dfa2fe37b/insilico_21_10662_i.fq.gz /var/lib/cwl/stgde9079ea-526b-4115-bffa-117b2fe48ab4/insilico_21_10663_i.fq.gz /var/lib/cwl/stg6af67b54-1db8-4d56-b45a-52b912e4c193/insilico_21_10664_i.fq.gz /var/lib/cwl/stg94136fad-e5cc-40e1-a86d-66c9770434cb/insilico_21_10665_i.fq.gz -real:544.19 -user:310.34 -sys:46.49 -pctCpu:65% -text:0k -data:0k -max:5529452k diff --git a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.md5 b/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.md5 deleted file mode 100644 index 8b13789..0000000 --- a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.md5 +++ /dev/null @@ -1 +0,0 @@ - diff --git a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.met b/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.met deleted file mode 100644 index 8460ad6..0000000 --- a/expected/cgpmap/cramOut/fq_gz_in/fq_gz_in.cram.met +++ /dev/null @@ -1,108 +0,0 @@ -# /opt/wtsi-cgp/biobambam2/bin/bammarkduplicates2 tmpfile=/var/spool/cwl/tmpMap_test/biormdup M=/var/spool/cwl/test.cram.met markthreads=27 level=0 - -##METRICS -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE -4471 0 500000 0 0 723 0 0.001446 172724026 - -## HISTOGRAM -BIN VALUE -1 1 -2 1.99711 -3 2.99134 -4 3.98269 -5 4.97118 -6 5.95681 -7 6.93959 -8 7.91953 -9 8.89664 -10 9.87092 -11 10.8424 -12 11.811 -13 12.7769 -14 13.74 -15 14.7003 -16 15.6578 -17 16.6125 -18 17.5645 -19 18.5137 -20 19.4602 -21 20.4039 -22 21.345 -23 22.2833 -24 23.2189 -25 24.1517 -26 25.0819 -27 26.0094 -28 26.9342 -29 27.8564 -30 28.7759 -31 29.6927 -32 30.6068 -33 31.5184 -34 32.4273 -35 33.3335 -36 34.2372 -37 35.1382 -38 36.0366 -39 36.9325 -40 37.8257 -41 38.7164 -42 39.6045 -43 40.49 -44 41.3729 -45 42.2534 -46 43.1312 -47 44.0065 -48 44.8793 -49 45.7496 -50 46.6174 -51 47.4826 -52 48.3454 -53 49.2056 -54 50.0634 -55 50.9187 -56 51.7715 -57 52.6218 -58 53.4697 -59 54.3152 -60 55.1582 -61 55.9987 -62 56.8368 -63 57.6725 -64 58.5058 -65 59.3367 -66 60.1652 -67 60.9913 -68 61.815 -69 62.6363 -70 63.4552 -71 64.2718 -72 65.086 -73 65.8979 -74 66.7074 -75 67.5146 -76 68.3194 -77 69.1219 -78 69.9221 -79 70.72 -80 71.5156 -81 72.3089 -82 73.0999 -83 73.8886 -84 74.675 -85 75.4591 -86 76.241 -87 77.0206 -88 77.798 -89 78.5731 -90 79.346 -91 80.1166 -92 80.885 -93 81.6512 -94 82.4152 -95 83.177 -96 83.9365 -97 84.6939 -98 85.4491 -99 86.2021 -100 86.9529