diff --git a/assets/dummy_file b/assets/dummy_file
new file mode 100644
index 0000000..e69de29
diff --git a/modules/local/assigntaxaspecies.nf b/modules/local/assigntaxaspecies.nf
index ae29078..c932d7a 100644
--- a/modules/local/assigntaxaspecies.nf
+++ b/modules/local/assigntaxaspecies.nf
@@ -1,89 +1,101 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process ASSIGNTAXASPECIES {
-    tag '$bam'
-    label 'process_me'
+    label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'biocontainers/YOUR-TOOL-HERE' }"
+    container "ghcr.io/h3abionet/tada:dev"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    path bam
-
+    path(st)
+    path(ref)
+    path(sp)
+    
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    path "*.bam", emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
-
+    path("tax_final.RDS"), emit: taxtab
+    path("bootstrap_final.RDS"), emit: bootstraps
+    
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    def runSpecies = sp.name != "dummy_file" ? "TRUE" : "FALSE"
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        $bam
+    #!/usr/bin/env Rscript
+    suppressPackageStartupMessages(library(dada2))
+
+    seqs <- readRDS("${st}")
+    seqtab <- seqs\$seq
+
+    # Assign taxonomy
+    tax <- NULL
+    boots <- NULL
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        assigntaxaspecies: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
+    if ( ${params.tax_batch} == 0 | length(seqtab) < ${params.tax_batch} ) { # no batch, run normally
+        cat("Running all samples\\n")
+        tax <- assignTaxonomy(seqtab, "${ref}",
+                        multithread=${task.cpus},
+                        tryRC = TRUE,
+                        outputBootstraps = TRUE,
+                        minBoot = ${params.min_boot},
+                        verbose = TRUE)
+        boots <- tax\$boot
+        if (${runSpecies}) {
+            tax <- addSpecies(tax, "${sp}",
+                 tryRC = TRUE,
+                 verbose = TRUE)
+        } else {
+            tax <- tax\$tax
+        }
+    } else {
+        # see https://github.com/benjjneb/dada2/issues/1429 for this
+        to_split <- seq(1, length(seqtab), by = ${params.tax_batch})
+        to_split2 <- c(to_split[2:length(to_split)]-1, length(seqtab))
+
+        for(i in 1:length(to_split)){
+            cat(paste("Running all samples from",to_split[i], "to", to_split2[i], "\\n"))
+            seqtab2 <- seqtab[to_split[i]:to_split2[i]]
+            tax2 <- assignTaxonomy(seqtab2, "${ref}",
+                    multithread=${task.cpus},
+                    tryRC = TRUE,
+                    outputBootstraps = TRUE,
+                    minBoot = ${params.min_boot},
+                    verbose = TRUE)
+
+            if (is.null(boots)) {
+                boots <- tax2\$boot
+            } else {
+                boots <- rbind(boots, tax2\$boot)
+            }
+
+            if (${runSpecies}) {
+                tax2 <- addSpecies(tax2\$tax, 
+                    refFasta = "${sp}", 
+                    tryRC = TRUE,
+                    verbose = TRUE)
+            } else {
+                tax2 <- tax2\$tax
+            }
+            if (is.null(tax)) {
+                tax <- tax2
+            } else {
+                tax <- rbind(tax, tax2)
+            }
+        }
+    }
+
+    # make sure these are the same order
+    # they should be, but we don't assume this
+    rownames(tax) <- seqs[rownames(tax),]\$id
+    rownames(boots) <- seqs[rownames(boots),]\$id
+
+    # Write original data
+    saveRDS(tax, "tax_final.RDS")
+    saveRDS(boots, "bootstrap_final.RDS")
     """
 
     stub:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        assigntaxaspecies: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
+    
     """
 }
diff --git a/modules/local/dadainfer.nf b/modules/local/dadainfer.nf
index 40f2f51..79ae2c9 100644
--- a/modules/local/dadainfer.nf
+++ b/modules/local/dadainfer.nf
@@ -8,8 +8,6 @@ process DADAINFER {
     tuple val(readmode), file(err), file(reads)
 
     output:
-    // TODO nf-core: List additional required output channels/values here
-    // path "versions.yml"           , emit: versions
     path("all.dd.${readmode}.RDS"), emit: inferred
 
     when:
@@ -52,11 +50,6 @@ process DADAINFER {
 
     stub:
     def args = task.ext.args ?: ''
-    
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
     # add some real stuff here
     touch all.dd.${readmode}.RDS
diff --git a/modules/local/decipher.nf b/modules/local/decipher.nf
index 7dafc2c..d150814 100644
--- a/modules/local/decipher.nf
+++ b/modules/local/decipher.nf
@@ -1,47 +1,13 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process DECIPHER {
-    tag '$bam'
-    label 'process_me'
+    label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'biocontainers/YOUR-TOOL-HERE' }"
+    container "ghcr.io/h3abionet/tada:dev"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    path bam
+    path(seqs)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    path "*.bam", emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+    path("aligned_seqs.fna"), optional: true, emit: alignment
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,41 +15,21 @@ process DECIPHER {
     script:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        $bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        decipher: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
+    #!/usr/bin/env Rscript
+    suppressPackageStartupMessages(library(dada2))
+    suppressPackageStartupMessages(library(DECIPHER))
+
+    seqs <- readDNAStringSet("${seqs}")
+    alignment <- AlignSeqs(seqs,
+               anchor=NA,
+               processors = ${task.cpus})
+    writeXStringSet(alignment, "aligned_seqs.fna")
     """
 
     stub:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        decipher: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/fasttree.nf b/modules/local/fasttree.nf
index 9297be2..1c035cc 100644
--- a/modules/local/fasttree.nf
+++ b/modules/local/fasttree.nf
@@ -1,89 +1,30 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process FASTTREE {
-    tag '$bam'
-    label 'process_m'
+    label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'biocontainers/YOUR-TOOL-HERE' }"
+    container "quay.io/biocontainers/fasttree:2.1.10--h14c3975_3"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    path bam
+    path(aln)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    path "*.bam", emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+    path("fasttree.newick"), emit: treeGTR
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
-    """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        $bam
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fasttree: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
+    """
+    OMP_NUM_THREADS=${task.cpus} FastTree -nt \\
+        -gtr -gamma -spr 4 -mlacc 2 -slownni \\
+        -out fasttree.newick \\
+        ${aln}
     """
 
     stub:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fasttree: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/filterandtrim.nf b/modules/local/filterandtrim.nf
index d5ce8e6..c626a78 100644
--- a/modules/local/filterandtrim.nf
+++ b/modules/local/filterandtrim.nf
@@ -1,67 +1,24 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process FILTERANDTRIM {
     tag "$meta.id"
     label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    // TODO: pin to a versioned docker instance
     container "ghcr.io/h3abionet/tada:dev"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
     tuple val(meta), path(reads)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    // tuple val(meta), path("*.fastq.gz"), emit: trimmed_reads
-    // tuple val(meta), path("*.txt"), emit: trimmed_report
     tuple val(meta), path("${meta.id}.R1.filtered.fastq.gz"), optional: true, emit: trimmed_R1
     tuple val(meta), path("${meta.id}.R2.filtered.fastq.gz"), optional: true, emit: trimmed_R2
     tuple val(meta), path("${meta.id}.R[12].filtered.fastq.gz"), optional: true, emit: trimmed
     path("*.trimmed.txt"), emit: trimmed_report
 
-    // TODO nf-core: List additional required output channels/values here
-    // path "versions.yml"           , emit: versions
-
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
     #!/usr/bin/env Rscript
     suppressPackageStartupMessages(library(dada2))
@@ -91,10 +48,6 @@ process FILTERANDTRIM {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
     touch ${prefix}.R1.filtered.fastq.gz
     touch ${prefix}.R2.filtered.fastq.gz
diff --git a/modules/local/learnerrors.nf b/modules/local/learnerrors.nf
index caaf4fe..45089e9 100644
--- a/modules/local/learnerrors.nf
+++ b/modules/local/learnerrors.nf
@@ -8,8 +8,6 @@ process LEARNERRORS {
     tuple val(readmode), file(reads)
 
     output:
-    // TODO nf-core: List additional required output channels/values here
-    // path "versions.yml"           , emit: versions
     tuple val(readmode), file("errors.${readmode}.RDS"), emit: error_models
     // path("errors.R[12].RDS"), emit: errorModelsPerSample
     path("${readmode}.err.pdf"), emit: pdf
@@ -65,10 +63,6 @@ process LEARNERRORS {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
     # TODO: make a proper stub
     """
diff --git a/modules/local/mergetrimtables.nf b/modules/local/mergetrimtables.nf
index 4d255dd..0f34f92 100644
--- a/modules/local/mergetrimtables.nf
+++ b/modules/local/mergetrimtables.nf
@@ -8,10 +8,6 @@ process MERGETRIMTABLES {
 
     output:
     path("all.trimmed.csv"), emit: trimmed_report
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    // tuple val(meta), path("*.bam"), emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    // path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -35,10 +31,6 @@ process MERGETRIMTABLES {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
     touch "all.trimmed.csv"
     """
diff --git a/modules/local/phangorn.nf b/modules/local/phangorn.nf
index c8a6ee4..d4ca35d 100644
--- a/modules/local/phangorn.nf
+++ b/modules/local/phangorn.nf
@@ -1,47 +1,15 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process PHANGORN {
-    tag '$bam'
-    label 'process_me'
+    label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'biocontainers/YOUR-TOOL-HERE' }"
+    container "ghcr.io/h3abionet/tada:dev"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    path bam
+    path(aln)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    path "*.bam", emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+    path("unrooted.phangorn.RDS"), emit: treeRDS
+    path("unrooted.phangorn.newick"), emit: tree
+    path("unrooted.phangorn.GTR.newick"), emit: treeGTR
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,41 +17,30 @@ process PHANGORN {
     script:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        $bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        phangorn: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
+    #!/usr/bin/env Rscript
+    suppressPackageStartupMessages(library(phangorn))
+
+    phang.align <- read.phyDat("${aln}",
+                                format = "fasta",
+                                type = "DNA")
+
+    dm <- dist.ml(phang.align)
+    treeNJ <- NJ(dm) # Note, tip order != sequence order
+    fit = pml(treeNJ, data=phang.align)
+    write.tree(fit\$tree, file = "unrooted.phangorn.newick")
+
+    ## negative edges length changed to 0!
+    fitGTR <- update(fit, k=4, inv=0.2)
+    fitGTR <- optim.pml(fitGTR, model="GTR", optInv=TRUE, optGamma=TRUE,
+                          rearrangement = "stochastic", control = pml.control(trace = 0))
+    saveRDS(fitGTR, "unrooted.phangorn.RDS")
+    write.tree(fitGTR\$tree, file = "unrooted.phangorn.GTR.newick")
     """
 
     stub:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        phangorn: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/plotqualityprofile.nf b/modules/local/plotqualityprofile.nf
index c0e8f10..111928a 100644
--- a/modules/local/plotqualityprofile.nf
+++ b/modules/local/plotqualityprofile.nf
@@ -1,20 +1,3 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process PLOTQUALITYPROFILE {
     tag "$meta.id"
     label 'process_low'
@@ -23,12 +6,6 @@ process PLOTQUALITYPROFILE {
     container "ghcr.io/h3abionet/tada:dev"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
     tuple val(meta), path(reads)
 
     output:
@@ -45,15 +22,6 @@ process PLOTQUALITYPROFILE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
     #!/usr/bin/env Rscript
     suppressPackageStartupMessages(library(dada2))
@@ -71,10 +39,6 @@ process PLOTQUALITYPROFILE {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
     touch ${prefix}.PDF
     """
diff --git a/modules/local/pooledseqtable.nf b/modules/local/pooledseqtable.nf
index 6185e22..d8ec902 100644
--- a/modules/local/pooledseqtable.nf
+++ b/modules/local/pooledseqtable.nf
@@ -8,11 +8,9 @@ process POOLEDSEQTABLE {
     path(filts)
 
     output:
-    path("seqtab.filtered.RDS"), emit: seqtable
-    path("all.merged.RDS"), optional: true, emit: merged
-    path("seqtab.full.RDS"), emit: seqtabQC// we keep this for comparison and possible QC    
-    // TODO nf-core: List additional required output channels/values here
-    // path "versions.yml"           , emit: versions
+    path("seqtab.filtered.RDS"), emit: filtered_seqtable
+    path("all.merged.RDS"), optional: true, emit: merged_seqs
+    path("seqtab.full.RDS"), emit: full_seqtable// we keep this for comparison and possible QC    
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/local/removechimeras.nf b/modules/local/removechimeras.nf
index a99f754..bd6b2c5 100644
--- a/modules/local/removechimeras.nf
+++ b/modules/local/removechimeras.nf
@@ -1,91 +1,41 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process REMOVECHIMERAS {
-    tag "$meta.id"
-    label 'process_me'
+    label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'biocontainers/YOUR-TOOL-HERE' }"
+    container "ghcr.io/h3abionet/tada:dev"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    tuple val(meta), path(bam)
+    path(st)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    tuple val(meta), path("*.bam"), emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+    path("seqtab.nonchim.RDS"), emit: nonchim_seqtable
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    chimOpts = params.removeBimeraDenovo_options ? ", ${params.removeBimeraDenovo_options}" : ""
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    def prefix = task.ext.prefix
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        -o ${prefix}.bam \\
-        -T $prefix \\
-        $bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        removechimeras: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
+    #!/usr/bin/env Rscript
+    suppressPackageStartupMessages(library(dada2))
+    st.all <- readRDS("${st}")
+
+    # Remove chimeras
+    seqtab <- removeBimeraDenovo(
+        st.all, 
+        method="consensus", 
+        multithread=${task.cpus}, 
+        verbose=TRUE ${chimOpts} 
+        )
+
+    saveRDS(seqtab, "seqtab.nonchim.RDS")
     """
 
     stub:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    def prefix = task.ext.prefix
     """
-    touch ${prefix}.bam
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        removechimeras: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/renameasvs.nf b/modules/local/renameasvs.nf
index 0ce3890..16574b6 100644
--- a/modules/local/renameasvs.nf
+++ b/modules/local/renameasvs.nf
@@ -1,47 +1,16 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process RENAMEASVS {
-    tag '$bam'
     label 'process_low'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'biocontainers/YOUR-TOOL-HERE' }"
+    container "ghcr.io/h3abionet/tada:dev"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    path bam
+    path(st)
+    path(rawst)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    path "*.bam", emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+    path("seqtab_final.${params.id_type}.RDS"), emit: seqtable_renamed
+    path("asvs.${params.id_type}.nochim.fna"), emit: nonchimeric_asvs
+    path("readmap.RDS"), emit: readmap
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,41 +18,46 @@ process RENAMEASVS {
     script:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        $bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        renameasvs: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
+    #!/usr/bin/env Rscript
+    suppressPackageStartupMessages(library(dada2))
+    suppressPackageStartupMessages(library(ShortRead))
+    suppressPackageStartupMessages(library(digest))
+
+    # read RDS w/ data
+    st <- readRDS("${st}")
+    st.raw <- readRDS("${rawst}")
+
+    # get sequences
+    seqs <- colnames(st)
+    seqs.raw <- colnames(st.raw)
+
+    # get IDs based on idType
+    ids_study <- switch("${params.id_type}", simple=paste("ASV", 1:ncol(st), sep = ""),
+                                md5=sapply(colnames(st), digest, algo="md5"))
+    ids_study.raw <- switch("${params.id_type}", simple=paste("ASV", 1:ncol(st.raw), sep = ""),
+                                md5=sapply(colnames(st.raw), digest, algo="md5"))
+
+    # sub IDs
+    colnames(st) <- unname(ids_study)
+    colnames(st.raw) <- unname(ids_study.raw)
+
+    # generate FASTA
+    seqs.dna <- ShortRead(sread = DNAStringSet(seqs), id = BStringSet(ids_study))
+    # Write out fasta file.
+    writeFasta(seqs.dna, file = 'asvs.${params.id_type}.nochim.fna')
+
+    seqs.dna.raw <- ShortRead(sread = DNAStringSet(seqs.raw), id = BStringSet(ids_study.raw))
+    writeFasta(seqs.dna.raw, file = 'asvs.${params.id_type}.raw.fna')
+
+    # Write modified data (note we only keep the no-chimera reads for the next stage)
+    saveRDS(st, "seqtab_final.${params.id_type}.RDS")
+    saveRDS(data.frame(id = ids_study, seq = seqs), "readmap.RDS")
     """
 
     stub:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        renameasvs: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
     """
 }
diff --git a/modules/local/roottree.nf b/modules/local/roottree.nf
index ea20d67..284dda1 100644
--- a/modules/local/roottree.nf
+++ b/modules/local/roottree.nf
@@ -1,47 +1,15 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process ROOTTREE {
-    tag '$bam'
-    label 'process_low'
+    label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'biocontainers/YOUR-TOOL-HERE' }"
+    container "ghcr.io/h3abionet/tada:dev"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    path bam
+    path(tree)
+    val(tree_tool)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    path "*.bam", emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+    path("rooted.${tree_tool}.newick"), emit: rooted_tree
+    path("rooted.${tree_tool}.RDS"), emit: rooted_tree_RDS
 
     when:
     task.ext.when == null || task.ext.when
@@ -49,41 +17,23 @@ process ROOTTREE {
     script:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        $bam
+    #!/usr/bin/env Rscript
+    suppressPackageStartupMessages(library(phangorn))
+    suppressPackageStartupMessages(library(ape))
+
+    tree <- read.tree(file = "${tree}")
+
+    midtree <- midpoint(tree)
+
+    write.tree(midtree, file = "rooted.${tree_tool}.newick")
+    saveRDS(midtree, "rooted.${tree_tool}.RDS")
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        roottree: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
     """
 
     stub:
     def args = task.ext.args ?: ''
     
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        roottree: \$(samtools --version |& sed '1!d ; s/samtools //')
-    END_VERSIONS
     """
 }
diff --git a/nextflow.config b/nextflow.config
index 419f5a9..ad7232b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -47,8 +47,8 @@ params {
     pacbio_strict_match = true
 
     // setting these assumes use of cutadapt for trimming
-    fwd_adapter = false 
-    rev_adapter = false
+    fwd_adapter = "" 
+    rev_adapter = ""
     trim_for = 0
     trim_rev = 0
     trunc_for = 0
@@ -80,14 +80,14 @@ params {
     min_asv_len = 0 // Only run if set > 1
     // Chimera detection
     chimera_detection = true
-    // removeBimeraDenovoOptions = false
+    removeBimeraDenovo_options = ""
 
     // Taxonomic assignment
     tax_assignment_method = 'rdp' // default: RDP classifier implementation in dada2
-    reference = false
-    species = false
+    reference = ""
+    species = ""
     min_boot = 50 // default for dada2
-    tax_levels = false
+    tax_levels = ""
     tax_batch = 0  // batch size of ASVs to run through assignTaxonomy/assignSpecies, 0 = run everything
 
     // alignment
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 75c9487..7c3cee8 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -437,6 +437,9 @@
         },
         "rescue_unmerged": {
             "type": "boolean"
+        },
+        "removeBimeraDenovo_options": {
+            "type": "string"
         }
     }
 }
\ No newline at end of file
diff --git a/workflows/tada.nf b/workflows/tada.nf
index 771a166..1dbb3e9 100644
--- a/workflows/tada.nf
+++ b/workflows/tada.nf
@@ -15,6 +15,15 @@ include { MERGETRIMTABLES        } from '../modules/local/mergetrimtables'
 include { LEARNERRORS            } from '../modules/local/learnerrors'
 include { DADAINFER              } from '../modules/local/dadainfer'
 include { POOLEDSEQTABLE         } from '../modules/local/pooledseqtable'
+include { REMOVECHIMERAS         } from '../modules/local/removechimeras'
+include { RENAMEASVS             } from '../modules/local/renameasvs'
+include { ASSIGNTAXASPECIES      } from '../modules/local/assigntaxaspecies'
+include { DECIPHER               } from '../modules/local/decipher'
+include { PHANGORN               } from '../modules/local/phangorn'
+include { FASTTREE               } from '../modules/local/fasttree'
+include { ROOTTREE               } from '../modules/local/roottree'
+
+
 include { paramsSummaryMap       } from 'plugin/nf-validation'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
@@ -104,11 +113,10 @@ workflow TADA {
     ch_trimmed_reads = FILTERANDTRIM.out.trimmed
     ch_reports = FILTERANDTRIM.out.trimmed_report.collect()
 
-    
     MERGETRIMTABLES(
         ch_reports
     )
-    
+
     // Channel setup
 
     // We need to group data depending on which downstream steps are needed.  There
@@ -122,7 +130,6 @@ workflow TADA {
     //    the two groups can be processed in parallel.  So we set up the channels with 
     //    this in mind. No sample ID info is really needed.
     ch_trimmed_infer = FILTERANDTRIM.out.trimmed_R1
-            // .concat(filteredReadsR2.ifEmpty([]))
             .map { [ 'R1', it[1]] }
             .concat(FILTERANDTRIM.out.trimmed_R2.map {['R2', it[1]] } )
             .groupTuple(sort: true)
@@ -142,6 +149,9 @@ workflow TADA {
     ch_infer = LEARNERRORS.out.error_models.join(ch_trimmed_infer)
 
     // this is always in pooled mode at the moment, should be adjusted
+
+    // if (params.pool == "T" || params.pool == 'pseudo') { 
+
     DADAINFER(
         ch_infer
     )
@@ -155,150 +165,62 @@ workflow TADA {
         DADAINFER.out.inferred.collect(),
         ch_trimmed
         )
-    // if (params.pool == "T" || params.pool == 'pseudo') { 
 
-        // process DadaInfer {
-        //     tag { "DadaInfer:${readmode}" }
-        //     publishDir "${params.outdir}/dada2-Derep-Pooled", mode: "copy", overwrite: true
-
-        //     input:
-        //     // DADA2 step runs on all R1 and/or on all R2
-        //     tuple val(readmode), file(err), file(reads) from errorModelsPooled
-        //         .join(ReadsInfer)
-
-        //     output:
-        //     // Note that the mode ('merged', 'R1', 'R2') can now potentially allow SE read analysis
-        //     file("all.dd.${readmode}.RDS") into dadaMerge,dadaToReadTracking
-
-        //     when:
-        //     params.precheck == false
-
-        //     script:
-        //     dadaOpt = !params.dadaOpt.isEmpty() ? "'${params.dadaOpt.collect{k,v->"$k=$v"}.join(", ")}'" : 'NA'
-        //     template "DadaPooled.R"
-        // }
-
-        // // This one is a little tricky. We can't know a priori how many instances of reads (R1 and R2) 
-        // // are present outside the process, but we can determine this internally within the process 
-        // // when we collect all of them.
-        // // So, here we check the size of the collected channel containing the denoised models; if 
-        // // there are two then this is a paired-end run, otherwise it's single-end. Logic is in the R script
-        
-        // process PooledSeqTable {
-        //     tag { "PooledSeqTable:${readmode}" }
-        //     publishDir "${params.outdir}/dada2-OriginalSeqTable", mode: "copy", overwrite: true
-
-        //     input:
-        //     // we don't care about the mode here, so only get the dds (dada-inferred) RDS files
-        //     file(dds) from dadaMerge.collect()
-        //     // we don't care about the mode here, we only grab the reads
-        //     file(filts) from ReadsMerge
-        //         .map { it[1] }
-        //         .flatten()
-        //         .collect()
-
-        //     output:
-        //     tuple val(readmode), file("seqtab.${readmode}.RDS") into seqTable,rawSeqTableToRename
-        //     file "all.merged.RDS" optional true into mergerTracking,mergerQC
-        //     file "seqtab.original.*.RDS" into seqtabQC// we keep this for comparison and possible QC
-
-        //     when:
-        //     params.precheck == false
-
-        //     script:
-        //     // We could switch this to 'paired' vs 'single-end' as well
-        //     readmode = dds.size() == 2 ? 'merged' : 'R1'
-        //     template "SeqTables.R"
-        // }
-    // } else {
-
-        // process PerSampleInferDerepAndMerge {
-        //     tag { "PerSampleInferDerepAndMerge:${meta.id}" }
-        //     publishDir "${params.outdir}/dada2-Derep-Single/Per-Sample", mode: "copy", overwrite: true
-
-        //     input:
-        //     tuple val(meta), file(reads) from readsToPerSample
-        //     file(errs) from errorModelsPerSample.collect()
-
-        //     output:
-        //     file("${meta.id}.{R1,merged}.RDS") into combinedReads
-        //     tuple val(meta), file("${meta.id}.dd.R{1,2}.RDS") into perSampleDadaToMerge
-        //     val(readmode) into modeSeqTable
-
-        //     when:
-        //     params.precheck == false
-
-        //     script:
-        //     dadaOpt = !params.dadaOpt.isEmpty() ? "'${params.dadaOpt.collect{k,v->"$k=$v"}.join(", ")}'" : 'NA'
-        //     readmode = errs.size() == 2 ? 'merged' : 'R1'
-        //     template "PerSampleDadaInfer.R"
-        // }
-
-        // process MergeDadaRDS {
-        //     tag { "mergeDadaRDS" }
-        //     publishDir "${params.outdir}/dada2-Derep-Single", mode: "copy", overwrite: true
-
-        //     input:
-        //     file(dds) from perSampleDadaToMerge
-        //                   .map { it[1] }
-        //                   .flatten()
-        //                   .collect()
-
-        //     output:
-        //     file("all.dd.R{1,2}.RDS") into dadaToReadTracking
-
-        //     when:
-        //     params.precheck == false
-
-        //     script:
-        //     template "MergePerSampleDada.R"
-        // }
-
-        // process SequenceTable {
-        //     tag { "SequenceTable:${readmode}" }
-        //     publishDir "${params.outdir}/dada2-Derep-Single", mode: "copy", overwrite: true
-
-        //     input:
-        //     file(mr) from combinedReads.collect()
-        //     val(readmode) from modeSeqTable.first()
-
-        //     output:
-        //     tuple val(readmode), file("seqtab.${readmode}.RDS") into seqTable,rawSeqTableToRename
-        //     file "all.merged.RDS" optional true into mergerTracking,mergerQC
-        //     file "seqtab.original.${readmode}.RDS" into seqtabQC // we keep this for comparison and possible QC
-            
-        //     when:
-        //     params.precheck == false
-
-        //     script:
-        //     template "PerSampleSeqTable.R"
-        // }
-    // }
+    REMOVECHIMERAS(
+        POOLEDSEQTABLE.out.filtered_seqtable
+    )
 
-    // } else if (params.seqTables) { // TODO maybe we should check the channel here
-    //     process MergeSeqTables {
-    //         tag { "MergeSeqTables" }
-    //         publishDir "${params.outdir}/dada2-MergedSeqTable", mode: 'copy'
+    RENAMEASVS(
+        REMOVECHIMERAS.out.nonchim_seqtable,
+        POOLEDSEQTABLE.out.filtered_seqtable
+    )
 
-    //         input:
-    //         file(st) from dada2SeqTabs
-    //                     .map { it[1] }
-    //                     .collect()
+    // Subworkflows-Taxonomic assignment (optional)
+    taxtab = Channel.empty()
+    if (params.reference) {
+        ref_file = file(params.reference, checkIfExists: true)
+        species_file = params.species ? file(params.species, checkIfExists: true) : file("${projectDir}/assets/dummy_file")
+
+        ASSIGNTAXASPECIES(
+            RENAMEASVS.out.readmap,
+            ref_file,
+            species_file
+        )
+        taxtab = ASSIGNTAXASPECIES.out.taxtab
+    }
+    
+    // Subworkflows-Alignment + Phylogenetic Tree (optional)
+    DECIPHER(
+        RENAMEASVS.out.nonchimeric_asvs
+    )
 
-    //         output:
-    //         tuple val("merged"), file("seqtab.merged.RDS") into seqTable, rawSeqTableToRename
+    ch_tree = Channel.empty()
+    ch_tool = Channel.empty()
+    // this seems like the sort of thing a function map 
+    // would be useful for...
+    if (params.run_tree == 'phangorn') {
+        PHANGORN(
+            DECIPHER.out.alignment
+        )
+        ch_tree = PHANGORN.out.treeGTR
+    } else if (params.run_tree == 'fasttree') {
+        FASTTREE(
+            DECIPHER.out.alignment
+        )
+        ch_tree = FASTTREE.out.treeGTR
+    } else {
+        // this needs to die with an error message, or
+        // it needs to be caught above
+    }
 
-    //         script:
-    //         template "MergeSeqTables.R"
-    //     }
-    //     Channel.empty().into { SEChimera;RawSEChimeraToRename;trimmedReadTracking;dadaToReadTracking;mergerTracking;mergerQC }
-    // }    
+    ROOTTREE(
+        ch_tree,
+        params.run_tree
+    )
 
-    // Subworkflows-Taxonomic assignment (optional)
+    // Subworkflows-Alternative outputs
 
-    // Subworkflows-Alignment + Phylogenetic Tree
 
-    // Subworkflows-Alternative outputs
 
     //
     // Collate and save software versions