From 7e23dd198eb79e1ecfa90a1ae078d00066254918 Mon Sep 17 00:00:00 2001 From: Emilio Palumbo Date: Mon, 31 Aug 2020 15:27:55 +0200 Subject: [PATCH] Update normalize_bam CI function and checksums --- .circ | 22 +++++++++++----------- data/gemflux.md5 | 6 +++--- data/ihec.md5 | 12 ++++++------ data/markdup.md5 | 12 ++++++------ data/rmdup.md5 | 12 ++++++------ data/starflux.md5 | 6 +++--- data/starrsem.md5 | 12 ++++++------ 7 files changed, 41 insertions(+), 41 deletions(-) diff --git a/.circ b/.circ index 7ae1071..30c6afd 100755 --- a/.circ +++ b/.circ @@ -9,7 +9,7 @@ _ci_usage() { clean remove the temporary directory used for vaildation Notes: - If '\$CI_DIR' is in the Nextflow asset folder the pipeline is run using the GitHub repository + If '\$CI_DIR' is in the Nextflow asset folder the pipeline is run using the GitHub repository to allow to change revision from the comand line, e.g.: CI_DIR=~/.nextflow/assets/guigolab/grape-nf ci test -r v0.4.1 @@ -23,12 +23,12 @@ _ci_canonicalize_path() { else _ci_canonicalize_file_path "$1" fi -} +} # Get canonical path of a directory _ci_canonicalize_dir_path() { - (cd "$1" 2>/dev/null && pwd -P) -} + (cd "$1" 2>/dev/null && pwd -P) +} # Get canonical path of a file _ci_canonicalize_file_path() { @@ -38,11 +38,11 @@ _ci_canonicalize_file_path() { (cd "$dir" 2>/dev/null && printf '%s/%s\n' "$(pwd -P)" "$file") } -# Check that Nextflow is installed and download it to the current +# Check that Nextflow is installed and download it to the current # folder otherwise _ci_setup_nxf() { if ! nextflow &>/dev/null; then - export PATH=$PWD:$PATH + export PATH=$PWD:$PATH if [ ! -x nextflow ]; then curl -fsSL get.nextflow.io | bash && chmod +x nextflow fi @@ -51,10 +51,10 @@ _ci_setup_nxf() { # Get the content of a BAM file for checksum _ci_normalize_bam() { - docker run --rm -v $1:$1 -w $PWD grapenf/samtools:1.3.1 bash -c "samtools view -h $2 | grep -v '@CO\|@PG' | samtools view -Sb - > $(basename $2) 2>/dev/null" + docker run --rm -v $CI_DIR:$CI_DIR -v $1:$1 -w $PWD grapenf/samtools:1.3.1 bash -c "samtools view -h $2 | grep -v '@CO\|@PG' | LC_ALL=C sort > $(basename $2) 2>/dev/null" } -# Get file to the CI output directory either by creating a symlink +# Get file to the CI output directory either by creating a symlink # or normalizing a BAM file _ci_get_file() { local baseDir=$1 @@ -95,7 +95,7 @@ _ci_check() { (mkdir -p $CI_OUTDIR && cd $CI_OUTDIR echo $CI_PROFILE > .ci_profile cut -f 3 ../pipeline.db | while read f - do + do _ci_get_file $(_ci_canonicalize_path ..) $f done md5sum -c ${CI_DIR}/data/$CI_PROFILE.md5) @@ -141,7 +141,7 @@ ci() { test) shift (_ci_test "$@");; - *) + *) _ci_usage;; esac } @@ -151,4 +151,4 @@ CI_DIR=$(_ci_get_script_dir $0) CI_LOG=pipeline-ci.log CI_PROFILE="starrsem" CI_OUTDIR="checksum" -CI_RUNOPTS=("-process.errorStrategy=terminate" "-with-docker") \ No newline at end of file +CI_RUNOPTS=("-process.errorStrategy=terminate" "-with-docker") diff --git a/data/gemflux.md5 b/data/gemflux.md5 index 1dd5ed0..cc43eee 100644 --- a/data/gemflux.md5 +++ b/data/gemflux.md5 @@ -1,21 +1,21 @@ 60e3b244d81b235f4da09c6d0a216413 sample1.contigs.bed 9b31baf13928228a90c34ed11100ea5a sample1.genes.gff 092b15fa6e2f0b16bbe3ac5a77706f39 sample1.isoforms.gtf -cfe300e64671bbdee6652ce92ae5a053 sample1_m4_n10_toGenome.bam +ccee0df1e95b1a37fdde16f5b84911ca sample1_m4_n10_toGenome.bam 4ec7f9268c5dcef3b537c88169f89e19 sample1.minusRaw.bw 7ae99c171a210009538ddcd0ca016d6c sample1.plusRaw.bw 3aab7ddeea72e1e9c383ef99e8cb6c51 sample1_stats.json 80c3892ceee10325d96ccab6f1e64557 sample2.contigs.bed 13a9a9480dbff4e9e70d60b46ddd9e89 sample2.genes.gff 8941bc59f0e957058c4535c9f33977cb sample2.isoforms.gtf -63ae7df24c69cc8e6cc17ad81cc36331 sample2_m4_n10_toGenome.bam +f0233b16d583f683b45bede3b23f4afa sample2_m4_n10_toGenome.bam 4c852dab27a29718d4393b9514b6ca41 sample2.minusRaw.bw e66ef8cf062e662d5975bef6cab7a645 sample2.plusRaw.bw fd49b1c19e153c8ee112609e1ce757a0 sample2_stats.json 89f19344b1f1a346a105f2b3f9443f9e sample3.contigs.bed 74f9de8e31ff2c24bc45af5f8ec73530 sample3.genes.gff 1a039c489fdeb3e0ab4ff768424b5997 sample3.isoforms.gtf -7a342ac43535d6f56492ea081f956779 sample3_m4_n10_toGenome.bam +5f321238975bdde3bd81aee70ccb1f77 sample3_m4_n10_toGenome.bam db10a50bb7eebec0f3421f4460d4cae8 sample3.minusRaw.bw 235e2d65c856c969048e432234c04ff4 sample3.plusRaw.bw 77c72bef6f1410e33c90dbc01697fffc sample3_stats.json diff --git a/data/ihec.md5 b/data/ihec.md5 index fcae99a..92066fb 100644 --- a/data/ihec.md5 +++ b/data/ihec.md5 @@ -1,8 +1,8 @@ 30245cd4c1b37b323a1428e6a79b6b46 sample1.contigs.bed 5dd20d4ee5a2c161536ef43460c3537a sample1.genes.results d2ce2685d81e4d3cafd42ff91284139c sample1.isoforms.results -a79f77a6ce5b6c1f47c38b1a038a4a50 sample1_m4_n10_toGenome.markdup.bam -33428e053dfb80aab625e422cb45aec6 sample1_m4_n10_toTranscriptome.bam +2dcd9d3a6981957cf9aee98e33658161 sample1_m4_n10_toGenome.markdup.bam +8d88fb9910efc782292322ab22ebff8c sample1_m4_n10_toTranscriptome.bam 2cbe0ae71670342704ecfbda2d64ac25 sample1_stats.json b8c92ab59a2366efef9342c762ad6aa3 sample1.Unique.minusRaw.bw 5a4ed2441202cb0ee4e1a8ce9842d7d4 sample1.UniqueMultiple.minusRaw.bw @@ -11,8 +11,8 @@ b461f2bde79dfeadcfbf49762937d584 sample1.Unique.plusRaw.bw 982947ea8922d0751a3e92407a14fe69 sample2.contigs.bed 134b79ef252a55eac18a282f990d881c sample2.genes.results 9935f541a76a39c53a3909f350fabb1f sample2.isoforms.results -fd65d80492ed977584d287b76df9d4fe sample2_m4_n10_toGenome.markdup.bam -db09bcc2983231ac2dca933837d1bdb5 sample2_m4_n10_toTranscriptome.bam +356564de835d5469c57eecb450b53fd3 sample2_m4_n10_toGenome.markdup.bam +001e4af88d8713bd610492ccf859f128 sample2_m4_n10_toTranscriptome.bam 5b99c51cc11b8dc0d0f41566a1459ca5 sample2_stats.json 99858805585a1dae5a247e39e5bb3943 sample2.Unique.minusRaw.bw b5197e0220965ebbda74b7d3b77558d7 sample2.UniqueMultiple.minusRaw.bw @@ -21,8 +21,8 @@ b5197e0220965ebbda74b7d3b77558d7 sample2.UniqueMultiple.minusRaw.bw 89f19344b1f1a346a105f2b3f9443f9e sample3.contigs.bed 568855cd154369988f0e9120660dcea6 sample3.genes.results a2ddfd7d7919830d69f941176ddff86f sample3.isoforms.results -b23e2d5f4a21ce71c27a82b768033883 sample3_m4_n10_toGenome.markdup.bam -6be11c68c6bfe99900982a848a7989bb sample3_m4_n10_toTranscriptome.bam +11e62a11f474ffa979ff9417c8d6c46b sample3_m4_n10_toGenome.markdup.bam +aa9845bc886d5f5183d123b481a22404 sample3_m4_n10_toTranscriptome.bam 93ac7fc04304459ca7f85472ab5b700f sample3_stats.json d7832747e6cc087ae631d22895adeac0 sample3.Unique.minusRaw.bw 0c15bda07bcb2f2424925b27f6394656 sample3.UniqueMultiple.minusRaw.bw diff --git a/data/markdup.md5 b/data/markdup.md5 index b81d832..92066fb 100644 --- a/data/markdup.md5 +++ b/data/markdup.md5 @@ -1,8 +1,8 @@ 30245cd4c1b37b323a1428e6a79b6b46 sample1.contigs.bed 5dd20d4ee5a2c161536ef43460c3537a sample1.genes.results d2ce2685d81e4d3cafd42ff91284139c sample1.isoforms.results -7991bd2774d8a9b6001c97fe45ab70e4 sample1_m4_n10_toGenome.markdup.bam -33428e053dfb80aab625e422cb45aec6 sample1_m4_n10_toTranscriptome.bam +2dcd9d3a6981957cf9aee98e33658161 sample1_m4_n10_toGenome.markdup.bam +8d88fb9910efc782292322ab22ebff8c sample1_m4_n10_toTranscriptome.bam 2cbe0ae71670342704ecfbda2d64ac25 sample1_stats.json b8c92ab59a2366efef9342c762ad6aa3 sample1.Unique.minusRaw.bw 5a4ed2441202cb0ee4e1a8ce9842d7d4 sample1.UniqueMultiple.minusRaw.bw @@ -11,8 +11,8 @@ b461f2bde79dfeadcfbf49762937d584 sample1.Unique.plusRaw.bw 982947ea8922d0751a3e92407a14fe69 sample2.contigs.bed 134b79ef252a55eac18a282f990d881c sample2.genes.results 9935f541a76a39c53a3909f350fabb1f sample2.isoforms.results -cae7766b2971d54dd96612385140f0c0 sample2_m4_n10_toGenome.markdup.bam -db09bcc2983231ac2dca933837d1bdb5 sample2_m4_n10_toTranscriptome.bam +356564de835d5469c57eecb450b53fd3 sample2_m4_n10_toGenome.markdup.bam +001e4af88d8713bd610492ccf859f128 sample2_m4_n10_toTranscriptome.bam 5b99c51cc11b8dc0d0f41566a1459ca5 sample2_stats.json 99858805585a1dae5a247e39e5bb3943 sample2.Unique.minusRaw.bw b5197e0220965ebbda74b7d3b77558d7 sample2.UniqueMultiple.minusRaw.bw @@ -21,8 +21,8 @@ b5197e0220965ebbda74b7d3b77558d7 sample2.UniqueMultiple.minusRaw.bw 89f19344b1f1a346a105f2b3f9443f9e sample3.contigs.bed 568855cd154369988f0e9120660dcea6 sample3.genes.results a2ddfd7d7919830d69f941176ddff86f sample3.isoforms.results -b23e2d5f4a21ce71c27a82b768033883 sample3_m4_n10_toGenome.markdup.bam -6be11c68c6bfe99900982a848a7989bb sample3_m4_n10_toTranscriptome.bam +11e62a11f474ffa979ff9417c8d6c46b sample3_m4_n10_toGenome.markdup.bam +aa9845bc886d5f5183d123b481a22404 sample3_m4_n10_toTranscriptome.bam 93ac7fc04304459ca7f85472ab5b700f sample3_stats.json d7832747e6cc087ae631d22895adeac0 sample3.Unique.minusRaw.bw 0c15bda07bcb2f2424925b27f6394656 sample3.UniqueMultiple.minusRaw.bw diff --git a/data/rmdup.md5 b/data/rmdup.md5 index c75af43..7042b90 100644 --- a/data/rmdup.md5 +++ b/data/rmdup.md5 @@ -1,8 +1,8 @@ 5afcc490a6b5717cf42c42ff093951be sample1.contigs.bed 5dd20d4ee5a2c161536ef43460c3537a sample1.genes.results d2ce2685d81e4d3cafd42ff91284139c sample1.isoforms.results -1ff1cfff22531c949f2db0b69488a03c sample1_m4_n10_toGenome.markdup.bam -33428e053dfb80aab625e422cb45aec6 sample1_m4_n10_toTranscriptome.bam +09eb9f6d52dc4decd5f78c41a7cee613 sample1_m4_n10_toGenome.markdup.bam +8d88fb9910efc782292322ab22ebff8c sample1_m4_n10_toTranscriptome.bam 788498a850584e3ab55218e626e032fe sample1_stats.json cff57373d6acc0a902058cadf06c17b2 sample1.Unique.minusRaw.bw f726544d2bd353c08c28adf3d81240b2 sample1.UniqueMultiple.minusRaw.bw @@ -11,8 +11,8 @@ c59cb9486bd2d3abe21d123e538e02b0 sample1.UniqueMultiple.plusRaw.bw bfc9a9c5501bbb0d1d60ee2b47a53916 sample2.contigs.bed 134b79ef252a55eac18a282f990d881c sample2.genes.results 9935f541a76a39c53a3909f350fabb1f sample2.isoforms.results -f762079c74bc01b3654b6cb2d62c1f1c sample2_m4_n10_toGenome.markdup.bam -db09bcc2983231ac2dca933837d1bdb5 sample2_m4_n10_toTranscriptome.bam +66bf139ee0e17a4ac24eb8ea58112c30 sample2_m4_n10_toGenome.markdup.bam +001e4af88d8713bd610492ccf859f128 sample2_m4_n10_toTranscriptome.bam b50b1fbf7a9d04bd78a1d5427f7356ae sample2_stats.json 7362829e0b4279f23a13c7e5546bd134 sample2.Unique.minusRaw.bw f1a2be88768194dfa2ad4cf3f3cfe496 sample2.UniqueMultiple.minusRaw.bw @@ -21,8 +21,8 @@ d14e02cf22f15c9d49af61d8fda1718a sample2.Unique.plusRaw.bw a14c5872ab9a2dcf55a70a7b17f449ea sample3.contigs.bed 568855cd154369988f0e9120660dcea6 sample3.genes.results a2ddfd7d7919830d69f941176ddff86f sample3.isoforms.results -1b979a874a8c1f5068a305dc6a216618 sample3_m4_n10_toGenome.markdup.bam -6be11c68c6bfe99900982a848a7989bb sample3_m4_n10_toTranscriptome.bam +a17775628cbaae90ec26687f98b417c5 sample3_m4_n10_toGenome.markdup.bam +aa9845bc886d5f5183d123b481a22404 sample3_m4_n10_toTranscriptome.bam bc7ecf0db0ed5b035fac07f521849de6 sample3_stats.json 811d8dde82e960f098854f2384507778 sample3.Unique.minusRaw.bw 8e197ae04a0f9b4ddee9ad7eaa43e396 sample3.UniqueMultiple.minusRaw.bw diff --git a/data/starflux.md5 b/data/starflux.md5 index a1b9d8c..820a0ee 100644 --- a/data/starflux.md5 +++ b/data/starflux.md5 @@ -1,7 +1,7 @@ 30245cd4c1b37b323a1428e6a79b6b46 sample1.contigs.bed 94884593db9b76caa87bf2c3b09c4671 sample1.genes.gff c3cfd6d32e8bd3258bb1cb6127157a99 sample1.isoforms.gtf -e1cf9e315706bf0eb08258d503a36274 sample1_m4_n10_toGenome.bam +62dcbc3b66c603e998a7e1f564e3743a sample1_m4_n10_toGenome.bam 6936e714ac8f98c951ba52ec8fd0e441 sample1_stats.json 37aa4ae5af33a81f8775440bbfd21fba sample1.Unique.minusRaw.bw ffce7ba84865e21df6bf8fb849822545 sample1.UniqueMultiple.minusRaw.bw @@ -10,7 +10,7 @@ b2d459ec4663d01769e97352c2b59de2 sample1.UniqueMultiple.plusRaw.bw 982947ea8922d0751a3e92407a14fe69 sample2.contigs.bed 342fe787dd63b159919b99f9223d00c9 sample2.genes.gff f2b8f02792b460063ab3dd9d74a0e460 sample2.isoforms.gtf -25d835f345f074934e63c5b6d87a77ab sample2_m4_n10_toGenome.bam +c3b825e524cd9143a85c46d3807a7c87 sample2_m4_n10_toGenome.bam 0295d0759fbf5a2df7035f8ff5333e5e sample2_stats.json 1de3717e5641e2eccd5f1c939c606f3d sample2.Unique.minusRaw.bw 3da795eb593185afb75c9aea84c82b87 sample2.UniqueMultiple.minusRaw.bw @@ -19,7 +19,7 @@ c7ad3d6214f976735c7e621b9f78d323 sample2.UniqueMultiple.plusRaw.bw 89f19344b1f1a346a105f2b3f9443f9e sample3.contigs.bed 74f9de8e31ff2c24bc45af5f8ec73530 sample3.genes.gff 1a039c489fdeb3e0ab4ff768424b5997 sample3.isoforms.gtf -7a342ac43535d6f56492ea081f956779 sample3_m4_n10_toGenome.bam +5f321238975bdde3bd81aee70ccb1f77 sample3_m4_n10_toGenome.bam 77c72bef6f1410e33c90dbc01697fffc sample3_stats.json 1363d4e278c9024433c2901996ab730a sample3.Unique.minusRaw.bw 2deb1fd284c866ff5faec6ceba351d56 sample3.UniqueMultiple.minusRaw.bw diff --git a/data/starrsem.md5 b/data/starrsem.md5 index f7f8ec3..171ccfa 100644 --- a/data/starrsem.md5 +++ b/data/starrsem.md5 @@ -1,8 +1,8 @@ 30245cd4c1b37b323a1428e6a79b6b46 sample1.contigs.bed 5dd20d4ee5a2c161536ef43460c3537a sample1.genes.results d2ce2685d81e4d3cafd42ff91284139c sample1.isoforms.results -e1cf9e315706bf0eb08258d503a36274 sample1_m4_n10_toGenome.bam -33428e053dfb80aab625e422cb45aec6 sample1_m4_n10_toTranscriptome.bam +62dcbc3b66c603e998a7e1f564e3743a sample1_m4_n10_toGenome.bam +8d88fb9910efc782292322ab22ebff8c sample1_m4_n10_toTranscriptome.bam 6936e714ac8f98c951ba52ec8fd0e441 sample1_stats.json 37aa4ae5af33a81f8775440bbfd21fba sample1.Unique.minusRaw.bw ffce7ba84865e21df6bf8fb849822545 sample1.UniqueMultiple.minusRaw.bw @@ -11,8 +11,8 @@ b2d459ec4663d01769e97352c2b59de2 sample1.UniqueMultiple.plusRaw.bw 982947ea8922d0751a3e92407a14fe69 sample2.contigs.bed 134b79ef252a55eac18a282f990d881c sample2.genes.results 9935f541a76a39c53a3909f350fabb1f sample2.isoforms.results -25d835f345f074934e63c5b6d87a77ab sample2_m4_n10_toGenome.bam -db09bcc2983231ac2dca933837d1bdb5 sample2_m4_n10_toTranscriptome.bam +c3b825e524cd9143a85c46d3807a7c87 sample2_m4_n10_toGenome.bam +001e4af88d8713bd610492ccf859f128 sample2_m4_n10_toTranscriptome.bam 0295d0759fbf5a2df7035f8ff5333e5e sample2_stats.json 1de3717e5641e2eccd5f1c939c606f3d sample2.Unique.minusRaw.bw 3da795eb593185afb75c9aea84c82b87 sample2.UniqueMultiple.minusRaw.bw @@ -21,8 +21,8 @@ c7ad3d6214f976735c7e621b9f78d323 sample2.UniqueMultiple.plusRaw.bw 89f19344b1f1a346a105f2b3f9443f9e sample3.contigs.bed 568855cd154369988f0e9120660dcea6 sample3.genes.results a2ddfd7d7919830d69f941176ddff86f sample3.isoforms.results -7a342ac43535d6f56492ea081f956779 sample3_m4_n10_toGenome.bam -6be11c68c6bfe99900982a848a7989bb sample3_m4_n10_toTranscriptome.bam +5f321238975bdde3bd81aee70ccb1f77 sample3_m4_n10_toGenome.bam +aa9845bc886d5f5183d123b481a22404 sample3_m4_n10_toTranscriptome.bam 77c72bef6f1410e33c90dbc01697fffc sample3_stats.json 1363d4e278c9024433c2901996ab730a sample3.Unique.minusRaw.bw 2deb1fd284c866ff5faec6ceba351d56 sample3.UniqueMultiple.minusRaw.bw