Stop using emu combine output

workflow/Snakefile

@@ -35,20 +35,17 @@ rule combine_outputs_split:
         abundances = ensure("results/emu_combined.tsv", non_empty=True),
     log:
         "logs/emu/combined_split.log",
-    params:
-        rank="tax_id",
-        extra="--counts",
     conda:
-        "envs/emu.yaml"
-    script:
-        "scripts/emu_combine.py"
+        "envs/dplyr.yaml"
+    shell:
+        "Rscript --vanilla workflow/scripts/combine_outputs.R {input} {output} 2>&1 | tee {log}"
 
 rule abundance:
     input:
         reads=f"{input_directory}{{sample}}{extension}",
         db=f"{database}",
     output:
-        abundances=temp("steps/emu_abundances/{sample}.tsv"),
+        abundances="steps/emu_abundances/{sample}.tsv",
         alignments=temp("steps/emu_abundances/{sample}_emu_alignments.sam"),
         unclassified= temp("steps/emu_abundances/{sample}_unclassified.fa"),
     log:

workflow/envs/dplyr.linux-64.pin.txt

@@ -0,0 +1,115 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
+https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2#19f9db5f4f1b7f5ef5f6d67207f25f38
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2024.2.2-hbcca054_0.conda#2f4327a1cbe7f022401b236e915a5fef
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2#0c96522c6bdaed4b1566d11387caaf45
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2#34893075a5c9e55cdafac56607368fc6
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2#4d59c254e01d9cde7957100457e2d5fb
+https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_1.conda#6185f640c43843e5ad6fd1c5372c3f80
+https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-2.6.32-he073ed8_17.conda#d731b543793afc0433c4fd593e693fce
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.40-h55db66e_0.conda#10569984e7db886e4f1abc2b47ad79a1
+https://conda.anaconda.org/conda-forge/noarch/libgcc-devel_linux-64-13.2.0-h95c4c6d_106.conda#960fa4aaa5c6a4733ac71954d835ce99
+https://conda.anaconda.org/conda-forge/noarch/libstdcxx-devel_linux-64-13.2.0-h95c4c6d_106.conda#aa932bbdb9cfea51e675f4b5a242ed6f
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-13.2.0-h95c4c6d_6.conda#3cfab3e709f77e9f1b3d380eb622494a
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2#f766549260d6815b0c52253f1fb1bb29
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-hc881cc4_6.conda#aae89d3736661c36a5591788aebd0817
+https://conda.anaconda.org/conda-forge/noarch/sysroot_linux-64-2.12-he073ed8_17.conda#595db67e32b276298ff3d94d07d47fbf
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
+https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.40-ha885e6a_0.conda#800a4c872b5bc06fa83888d112fe6c4f
+https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2#fee5683a3f04bd15cbd8318b096a27ab
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-hc881cc4_6.conda#df88796bd09a0d2ed292e59101478ad8
+https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hd590300_5.conda#69b8b6202a07720f448be700e300ccf4
+https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.28.1-hd590300_0.conda#dcde58ff9a1f30b0037a2315d1846d1f
+https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.10-h36c2ea0_0.tar.bz2#ac7bc6a654f8f41b352b38f4051135f8
+https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda#985f2f453fb72408d6b6f1be0f324033
+https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c
+https://conda.anaconda.org/conda-forge/linux-64/icu-73.2-h59595ed_0.conda#cc47e1facc155f91abd89b11e48e72ff
+https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.1-h166bdaf_0.tar.bz2#30186d27e2c9fa62b45fb1476b7200e3
+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f
+https://conda.anaconda.org/conda-forge/linux-64/libasprintf-0.22.5-h661eb56_2.conda#dd197c968bf9760bba0031888d431ede
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda#8e88f9389f1165d7c0936fe40d9a9a79
+https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172bf1cd1ff8629f2b1179945ed45055
+https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.2-h59595ed_0.conda#e7ba12deb7020dd080c6c70e7b6f6a3d
+https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
+https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-0.22.5-h59595ed_2.conda#172bcc51059416e7ce99e7b528cede83
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran5-13.2.0-h43f5ff8_6.conda#e54a5ddc67e673f9105cf2a2e9c070b0
+https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e
+https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8
+https://conda.anaconda.org/conda-forge/linux-64/libsanitizer-13.2.0-h95c4c6d_6.conda#be66a394ae0eb4bbeba5bba54e83ce53
+https://conda.anaconda.org/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda#40b61aab5c7ba9ff276c41cfffe6b80b
+https://conda.anaconda.org/conda-forge/linux-64/libwebp-base-1.4.0-hd590300_0.conda#b26e8aa824079e1be0294e7152ca4559
+https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.2.13-hd590300_5.conda#f36c115f1ee199da648e0597ec2047ad
+https://conda.anaconda.org/conda-forge/linux-64/make-4.3-hd18ef5c_1.tar.bz2#4049ebfd3190b580dffe76daed26155a
+https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.4.20240210-h59595ed_0.conda#97da8860a0da5413c7c98a3b3838a645
+https://conda.anaconda.org/conda-forge/linux-64/openssl-3.2.1-hd590300_1.conda#9d731343cff6ee2e5a25c4a091bf8e2a
+https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda#71004cbf7924e19c02746ccde9fd7123
+https://conda.anaconda.org/conda-forge/linux-64/pthread-stubs-0.4-h36c2ea0_1001.tar.bz2#22dad4df6e8630e8dff2428f6f6a7036
+https://conda.anaconda.org/conda-forge/linux-64/sed-4.8-he412f7d_0.tar.bz2#7362f0042e95681f5d371c46c83ebd08
+https://conda.anaconda.org/conda-forge/linux-64/xorg-kbproto-1.0.7-h7f98852_1002.tar.bz2#4b230e8381279d76131116660f5a241a
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libice-1.1.1-hd590300_0.conda#b462a33c0be1421532f28bfe8f4a7514
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxau-1.0.11-hd590300_0.conda#2c80dc38fface310c9bd81b17037fee5
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxdmcp-1.1.3-h7f98852_0.tar.bz2#be93aabceefa2fac576e971aef407908
+https://conda.anaconda.org/conda-forge/linux-64/xorg-renderproto-0.11.1-h7f98852_1002.tar.bz2#06feff3d2634e3097ce2fe681474b534
+https://conda.anaconda.org/conda-forge/linux-64/xorg-xextproto-7.3.0-h0b41bf4_1003.conda#bce9f945da8ad2ae9b1d7165a64d0f87
+https://conda.anaconda.org/conda-forge/linux-64/xorg-xproto-7.0.31-h7f98852_1007.tar.bz2#b4a4381d54784606820704f7b5f05a15
+https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
+https://conda.anaconda.org/conda-forge/linux-64/expat-2.6.2-h59595ed_0.conda#53fb86322bdb89496d7579fe3f02fd61
+https://conda.anaconda.org/conda-forge/linux-64/gcc_impl_linux-64-13.2.0-h1d3d475_6.conda#fb523fa3954d16178f7df937af68544f
+https://conda.anaconda.org/conda-forge/linux-64/libasprintf-devel-0.22.5-h661eb56_2.conda#02e41ab5834dcdcc8590cf29d9526f50
+https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20191231-he28a2e2_2.tar.bz2#4d331e44109e3f0e19b4cb8f9b82f3e1
+https://conda.anaconda.org/conda-forge/linux-64/libgettextpo-devel-0.22.5-h59595ed_2.conda#b63d9b6da3653179a278077f0de20014
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-13.2.0-h69a702a_6.conda#3666a850342f8f3be88f9a93d948d027
+https://conda.anaconda.org/conda-forge/linux-64/libnghttp2-1.58.0-h47da74e_1.conda#700ac6ea6d53d5510591c4344d5c989a
+https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.43-h2797004_0.conda#009981dd9cfcaa4dbfa25ffaed86bcae
+https://conda.anaconda.org/conda-forge/linux-64/libssh2-1.11.0-h0841786_0.conda#1f5a58e686b13bcfde88b93f547d23fe
+https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.15-h0b41bf4_0.conda#33277193f5b92bad9fdd230eb700929c
+https://conda.anaconda.org/conda-forge/linux-64/pcre2-10.42-hcad00b1_0.conda#679c8961826aa4b50653bce17ee52abe
+https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
+https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.4-h7391055_0.conda#93ee23f12bc2e684548181256edd2cf6
+https://conda.anaconda.org/conda-forge/linux-64/zlib-1.2.13-hd590300_5.conda#68c34ec6149623be41a1933ab996a209
+https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda#04b88013080254850d6c01ed54810589
+https://conda.anaconda.org/conda-forge/linux-64/bwidget-1.9.14-ha770c72_1.tar.bz2#5746d6202ba2abad4a4707f2a2462795
+https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
+https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda#219ba82e95d7614cf7140d2a4afc0926
+https://conda.anaconda.org/conda-forge/linux-64/gfortran_impl_linux-64-13.2.0-h0a8b748_6.conda#4aa3098203a4c5ba119978e27bafae8b
+https://conda.anaconda.org/conda-forge/linux-64/gxx_impl_linux-64-13.2.0-h1d3d475_6.conda#a7bdc9ce437d0958ebf0d2c7cf09d770
+https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.2-h659d440_0.conda#cd95826dbd331ed1be26bdf401432844
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.27-pthreads_h413a1c8_0.conda#a356024784da6dfd4683dc5ecf45b155
+https://conda.anaconda.org/conda-forge/linux-64/libtiff-4.6.0-h1dd3fc0_3.conda#66f03896ffbe1a110ffda05c7a856504
+https://conda.anaconda.org/conda-forge/linux-64/tktable-2.10-h0c5db8f_5.conda#9464044754ea25557a9c93f0327d90a6
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.9-h8ee46fc_0.conda#077b6e8ad6a3ddb741fce2496dd01bec
+https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.14.2-h14ed4e7_0.conda#0f69b688f52ff6da70bccb7ff7001d1d
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda#1a2a0cd3153464fee6646f3dd6dad9b8
+https://conda.anaconda.org/conda-forge/linux-64/libcurl-8.7.1-hca28451_0.conda#755c7f876815003337d2c61ff5d047e5
+https://conda.anaconda.org/conda-forge/linux-64/libglib-2.78.4-h783c2da_0.conda#d86baf8740d1a906b9716f2a0bac2f2d
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxext-1.3.4-h0b41bf4_2.conda#82b6df12252e6f32402b96dacc656fec
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxrender-0.9.11-hd590300_0.conda#ed67c36f215b310412b2af935bf3e530
+https://conda.anaconda.org/conda-forge/linux-64/xorg-libxt-1.3.0-hd590300_1.conda#ae92aab42726eb29d16488924f7312cb
+https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.0-h3faef2a_0.conda#f907bb958910dc404647326ca80c263e
+https://conda.anaconda.org/conda-forge/linux-64/curl-8.7.1-hca28451_0.conda#d2dd5466be2ce818f8097847341da63d
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-22_linux64_openblas.conda#b083767b6c877e24ee597d93b87ab838
+https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-8.3.0-h3d44ed6_0.conda#5a6f6c00ef982a9bc83558d9ac8f64a0
+https://conda.anaconda.org/conda-forge/linux-64/pango-1.52.1-ha41ecd1_0.conda#5c0cc002bf4eaa56448b0729efd6e96c
+https://conda.anaconda.org/conda-forge/linux-64/r-base-4.3.3-hb8ee39d_0.conda#261cd84cebc431aede55893365f1b178
+https://conda.anaconda.org/conda-forge/linux-64/r-cli-3.6.2-r43ha503ecb_0.conda#7a325f68b1354c1a5261688b5e54d008
+https://conda.anaconda.org/conda-forge/noarch/r-crayon-1.5.2-r43hc72bb7e_2.conda#f13cc355add93ff41ef3d7aeefee247a
+https://conda.anaconda.org/conda-forge/linux-64/r-fansi-1.0.6-r43h57805ef_0.conda#c94b12c76504df3548707218409b678f
+https://conda.anaconda.org/conda-forge/noarch/r-generics-0.1.3-r43hc72bb7e_2.conda#bf424d7238a8a02bd3970346112de34f
+https://conda.anaconda.org/conda-forge/linux-64/r-glue-1.7.0-r43h57805ef_0.conda#20e2cb7c0d27bccf8fe21ec5c3897751
+https://conda.anaconda.org/conda-forge/linux-64/r-magrittr-2.0.3-r43h57805ef_2.conda#7b04cb810f47eb12efc2e9be5f8ca1f1
+https://conda.anaconda.org/conda-forge/noarch/r-pkgconfig-2.0.3-r43hc72bb7e_3.conda#8978eef741fffaa48be070693a17f42f
+https://conda.anaconda.org/conda-forge/noarch/r-r6-2.5.1-r43hc72bb7e_2.conda#79f167972554dc6b65aa099cd85c22a1
+https://conda.anaconda.org/conda-forge/linux-64/r-rlang-1.1.3-r43ha503ecb_0.conda#0d71deb3b174a2876004ddcb6a4c7cfc
+https://conda.anaconda.org/conda-forge/linux-64/r-utf8-1.2.4-r43h57805ef_0.conda#d228498392dce22d3fe6266554498493
+https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.0-r43hc72bb7e_0.conda#7380a50d9daae38b40777f7630b8c3ba
+https://conda.anaconda.org/conda-forge/linux-64/r-ellipsis-0.3.2-r43h57805ef_2.conda#10c5892991072cfa3a61489d2ac6ad66
+https://conda.anaconda.org/conda-forge/noarch/r-lifecycle-1.0.4-r43hc72bb7e_0.conda#291d2fb68ea1b181644b40d6743ae000
+https://conda.anaconda.org/conda-forge/linux-64/r-vctrs-0.6.5-r43ha503ecb_0.conda#e398bd0451e6350a876a8561f8e90682
+https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.9.0-r43hc72bb7e_1.conda#7cff01456566a69381d3907d520c10b2
+https://conda.anaconda.org/conda-forge/noarch/r-tidyselect-1.2.1-r43hc72bb7e_0.conda#553c585e7874ffee2e2524094afaf1da
+https://conda.anaconda.org/conda-forge/linux-64/r-tibble-3.2.1-r43h57805ef_2.conda#afa7d3f21fbc5a2fbaa48cb9bacb7bce
+https://conda.anaconda.org/conda-forge/linux-64/r-dplyr-1.1.4-r43ha503ecb_0.conda#7ca8b417326d45b2e4bbf7429a0f1a7b

workflow/envs/dplyr.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - conda-forge::r-dplyr=1.1.4

workflow/scripts/combine_outputs.R

@@ -0,0 +1,30 @@
+# Get list of files from command line
+library(dplyr)
+args <- commandArgs(trailingOnly = TRUE)
+infiles <- args[1:length(args)-1]
+outfile <- args[length(args)]
+# Read all TSV files into dataframes and combine them
+samples_names <- gsub(".tsv", "", basename(infiles))
+process_file <- function(infile) {
+    sample_name <- gsub(".tsv", "", basename(infile))
+    df <- infile %>%
+        read.table(, header = TRUE, sep = "\t", stringsAsFactors = FALSE) %>% 
+        select(-abundance)
+    # Replace estimated.counts with sample name
+    colnames(df)[grep("estimated.counts", colnames(df))] <- sample_name
+    df
+}
+dfs <- lapply(infiles, process_file)
+
+
+#  Combine all dataframes into one using left_join with all columns that are not samples_names as keys
+taxa_cols <- setdiff(colnames(dfs[[1]]), samples_names)
+combined_df <- do.call(\(x, y) dplyr::full_join(x, y, by = taxa_cols), dfs)
+# Replace NA with 0 for every column in samples_names
+replace_na <- function(x) {
+    x[is.na(x)] <- 0
+    x
+}
+combined_df[samples_names] <- lapply(combined_df[samples_names], replace_na)
+# Write combined dataframe to file
+write.table(combined_df, outfile, sep = "\t", row.names = FALSE)